Search results for the GEO ID: GSE7291  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM174654 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 1
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
untreated K422 control cells
|
| Sample_geo_accession | GSM174654
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated control
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174654/suppl/GSM174654.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174657 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 2
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
untreated K422 control cells
|
| Sample_geo_accession | GSM174657
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated control
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174657/suppl/GSM174657.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174658 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 3
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
untreated K422 control cells
|
| Sample_geo_accession | GSM174658
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated control
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174658/suppl/GSM174658.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174659 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 4
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
untreated K422 control cells
|
| Sample_geo_accession | GSM174659
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated control
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174659/suppl/GSM174659.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174660 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab control 5
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
untreated K422 control cells
|
| Sample_geo_accession | GSM174660
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | untreated control
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174660/suppl/GSM174660.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174661 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 1
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174661
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174661/suppl/GSM174661.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174662 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 2
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174662
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174662/suppl/GSM174662.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174663 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 3
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174663
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174663/suppl/GSM174663.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174664 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 4
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174664
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174664/suppl/GSM174664.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174665 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 46 min, sample 5
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174665
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174665/suppl/GSM174665.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174672 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 1
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174672
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174672/suppl/GSM174672.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174673 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 2
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174673
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174673/suppl/GSM174673.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174674 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 3
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174674
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174674/suppl/GSM174674.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174675 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 4
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174675
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174675/suppl/GSM174675.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174676 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 100 µCi, 24 h, sample 5
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174676
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 100 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174676/suppl/GSM174676.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174677 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 1
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174677
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174677/suppl/GSM174677.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174690 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 2
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174690
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174690/suppl/GSM174690.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174691 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 3
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174691
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174691/suppl/GSM174691.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174692 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 4
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174692
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174692/suppl/GSM174692.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174693 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 46 min, sample 5
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174693
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 46 minutes (one half life time) at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174693/suppl/GSM174693.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174694 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 1
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174694
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174694/suppl/GSM174694.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174695 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 2
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174695
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174695/suppl/GSM174695.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174696 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 3
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174696
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174696/suppl/GSM174696.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174697 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 4
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174697
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174697/suppl/GSM174697.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
GSM174698 | GPL201 |
|
Alpha-irradiation with the radioimmuno-conjugate Bi-213-CD20-Rituximab 200 µCi, 24 h, sample 5
|
Cell line Karpas 422 (K422)
|
derived from a 73 year old woman with a B cell non-hodgkin´s lymphoma
|
Bi-213-CD20-Rituximab irradiated K422 cells
|
| Sample_geo_accession | GSM174698
| | Sample_status | Public on Jul 01 2007
| | Sample_submission_date | Mar 12 2007
| | Sample_last_update_date | Mar 20 2007
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The alpha-emitter Bi-213 was conjugated with CHX-A’’-DTPA-chelated CD20 antibody Rituximab.
| | Sample_treatment_protocol_ch1 | Subsequently the purified Bi-213-labelled antibody was added to the K422 cell suspension.
| | Sample_treatment_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml with an activity of Bi-213-CD20 of 200 µCi for 24 hours at 37°C, 5% CO2, 95% humidity.
| | Sample_growth_protocol_ch1 | A constant number of 1x106 K422 cells were incubated in a final volume of 2 ml RPMI 1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 1% penicilline/streptomycine and 1% L-glutamine at 37°C, 5% CO2, 95% humidity.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA of alpha irradiated K422 cells was extracted using the RNeasy Micro- Kit (Qiagen, Santa Clarita, CA, USA Cat. No. 74004). All buffers and solutions are part of the kit and were applied according to the manufacturer’s instructions. Briefly:
| | Sample_extract_protocol_ch1 | Alpha irradiated cells suspended in 350 µl lysis buffer were incubated with 350 µl 70%
| | Sample_extract_protocol_ch1 | ethanol. 700 µl suspension was put on RNeasy MinElute- column and spun down for one
| | Sample_extract_protocol_ch1 | minute with 10,000 rpm. One washing step with 350 µl RW1 buffer
| | Sample_extract_protocol_ch1 | DNase- digestion (10 µl DNase+70 µl RDD buffer for each sample) for 15 minutes at room temperature. 2 washing steps with 350 µl RW1- buffer and one step with 500 µl RPE- buffer.
| | Sample_extract_protocol_ch1 | 500 µl of 80% ethanol were put on RNeasy MinElute- column and spun down for 2
| | Sample_extract_protocol_ch1 | minutes with 10,000 rpm. Removal of ethanol: column was spun down for 5 minutes with 13,000 rpm. Elution of RNA with 14 µl of RNAse free water.
| | Sample_extract_protocol_ch1 | Quality and quantity control of the RNA using a Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto CA) and the NanoDrop ND-1000 (PeqLab Biotechnologie
| | Sample_extract_protocol_ch1 | GmbH, Erlangen). Purified RNA was stored at -80°C.
| | Sample_label_ch1 | Biotin/Streptavidin-PE
| | Sample_label_protocol_ch1 | Amplification, reverse transcription and labelling of the
| | Sample_label_protocol_ch1 | sample. For amplification of the RNA of the irradiated cells, the MessageAmp™ aRNA Kit (Ambion, Austin, TX, USA) was used. 500 ng of isolated RNA were transcribed into cDNA.
| | Sample_label_protocol_ch1 | First strand cDNA- Synthesis: 11 µl (RNA or RNA and dH2O) Sample
| | Sample_label_protocol_ch1 | 1 µl Oligo(dT)Primer 70°C incubation for 10 minutes, put on ice and incubated with the reaction kit (stated below).
| | Sample_label_protocol_ch1 | Reaction kit:
| | Sample_label_protocol_ch1 | 2 µl 10x First Strand Buffer
| | Sample_label_protocol_ch1 | 1 µl Ribonuclease Inhibitor
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | Adding 1µl Reverse transcriptase and 2 h incubation at 42°C
| | Sample_label_protocol_ch1 | Second strand cDNA- Synthesis:
| | Sample_label_protocol_ch1 | 63 µl Nuclease-free Water
| | Sample_label_protocol_ch1 | 10 µl 10x Second Strand Buffer
| | Sample_label_protocol_ch1 | 4 µl dNTP Mix
| | Sample_label_protocol_ch1 | 1 µl RNase H
| | Sample_label_protocol_ch1 | For second strand sythesis 2 µl of DNA- Polymerase are added followed by a 2 h
| | Sample_label_protocol_ch1 | Incubation step at 42°C.
| | Sample_label_protocol_ch1 | Purification of cDNA:
| | Sample_label_protocol_ch1 = Final elution volume | 16 µl and storage for 12 h at -20°C
| | Sample_label_protocol_ch1 | Labelling with in vitro transcription using biotin labelled nucleotides:
| | Sample_label_protocol_ch1 | Labeling mix:
| | Sample_label_protocol_ch1 | 4µl biotinylated dNTPs (Bio Array High Yield RNA Transcript Labelling Kit,
| | Sample_label_protocol_ch1 | Enzo Life Sciences, Farmingdale)
| | Sample_label_protocol_ch1 | 4 µl T7 10x reaction buffer
| | Sample_label_protocol_ch1 | 12 µl RNase free water
| | Sample_label_protocol_ch1 | The labelling mix is incubated with the sample and 4 µl of the enzyme mix is
| | Sample_label_protocol_ch1 | added followed by an incubation period of 5 hours at 37°C. The amplified RNA
| | Sample_label_protocol_ch1 | is purified and is eluted in a final volume of 96 µl.
| | Sample_label_protocol_ch1 | Quality control of aRNA:
| | Sample_label_protocol_ch1 | The concentration and purity of aRNA is measured using the NanoDrop ND-1000
| | Sample_label_protocol_ch1 | (PeqLab Biotechnologie GmbH, Erlangen) measuring absorptions at 260 and 280nm
| | Sample_label_protocol_ch1 | The OD 260/OD 280 aRNA was between 1.8 and 2,1. To exclude
| | Sample_label_protocol_ch1 | degradation and/or contamination RNA was analyzed again using an Agilent 2100
| | Sample_label_protocol_ch1 | Bioanalyzer (Agilent Technologies, Palo Alto CA).
| | Sample_label_protocol_ch1 | Fragmentation:
| | Sample_label_protocol_ch1 | For optimal hybridization with the complementary oligonucleodid sequences, a
| | Sample_label_protocol_ch1 | fragmentation of the amplified RNA was performed.
| | Sample_label_protocol_ch1 | 24 µl of the sample were added to 6 µl of fragmentation buffer (200 mM
| | Sample_label_protocol_ch1 | TRIS-Acetat, ph 8.2, 500 mM KOAc, 150 mM MgOAc, Affymetrix) and incubated at
| | Sample_label_protocol_ch1 | 94°C for 35 minutes.
| | Sample_hyb_protocol | Arrays were prehybridizised for 10 minutes using 140 µl
| | Sample_hyb_protocol | MES- hybridization buffer (70,4 g MES free acid monohydrate, 193.3 g MES Sodium
| | Sample_hyb_protocol | Salt, 800 ml accugen water, pH 6.5 – 6.7) and 140 µl aqua dest. at 45°C and 60 rpm in the Gene Chip® Hybridizing oven 640 (Affymetrix).
| | Sample_hyb_protocol | After removal of the pre-hybridizing solution, the array was loaded with 250 µl
| | Sample_hyb_protocol | of the hybridizing solution (30 µl fragmented aRNA, 5 µl control-oligo B2, 15 µl
| | Sample_hyb_protocol | 20x Eukaryotic hybridizing control, 3 µl salmon sperm-DNA, 3 µl acetylic BSA,
| | Sample_hyb_protocol | 150 µl 2x MES- Hybridizing buffer and 94 µl aqua dest.).
| | Sample_hyb_protocol | Following 16-hour incubation at 45°C with permanent rotation, the hybridizing
| | Sample_hyb_protocol | solution is removed.
| | Sample_hyb_protocol | The array was loaded with 280 µl of washing buffer A (300 ml 20x SSPE, 1ml 10%
| | Sample_hyb_protocol | Tween 20, 698 ml accugen water) and a maximum of 4 hybridized arrays are put
| | Sample_hyb_protocol | into the wash station ((Gene Chip® Fluidics, Affymetrix) with buffer A and buffer B
| | Sample_hyb_protocol | (83.3 ml 12x MES, 5.2 ml 5M NaCl, 1ml 10% Tween 20, 910.5 ml accugen water)
| | Sample_hyb_protocol | using the washing protocol which is prescribed by Affymetrix (for Human Genome Focus
| | Sample_hyb_protocol = Oligonukleotid- Arrays | Midi-euk2v3).
| | Sample_hyb_protocol | During washing procedure the staining solution is prepared:
| | Sample_hyb_protocol | Staining solution:
| | Sample_hyb_protocol | 600 µl 2x Staining Buffer
| | Sample_hyb_protocol | 540 µl dH2O
| | Sample_hyb_protocol | 48 µl BSA
| | Sample_hyb_protocol | 12 µl Streptavidine-Phycoerythrin-Conjugate
| | Sample_hyb_protocol | Array was incubated with 600 µl of the staining solution after washing for 40
| | Sample_hyb_protocol | minutes followed by incubation with the antibody solution for 10 minutes:
| | Sample_hyb_protocol | Antibody solution:
| | Sample_hyb_protocol | 300 µl 2x Staining Buffer 266
| | Sample_hyb_protocol | 4 µl dH2O
| | Sample_hyb_protocol | 24 µl BSA
| | Sample_hyb_protocol | 6 µl Goat IgG
| | Sample_hyb_protocol | 3.6 µl biotinylated Anti- Streptavidin- antibody
| | Sample_hyb_protocol | After removal of the antibody solution 600 µl of the staining solution is applied again for 10 minutes followed by removal of the staining solution and washing.
| | Sample_scan_protocol | The scanning of the array was performed using a GeneArray® 2500 Scanner (Affymetrix, Software GCOS[GeneChip Operating System]). Excitation of the fluorochrome
| | Sample_scan_protocol | phycoerythrin at a wave length of 488 nm with an emission at 570 nm.
| | Sample_data_processing | Using the affy package of functions of statistical scripting
| | Sample_data_processing | language 'R' integrated into the Bioconductor project data from cel files of
| | Sample_data_processing | each sample were normalized by variance stabilizing transformations (VSN)
| | Sample_data_processing | Ref.: Huber W, von Heydebreck A, Sultmann H, et al. Bioinformatics
| | Sample_data_processing | 2002;18:96-104.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Sascha,,Raschke
| | Sample_contact_laboratory | Hämatologisches Forschungslabor Geb. 23.12.00.62
| | Sample_contact_department | Klinik für Hämatologie, Onkologie und klinische Immunologie
| | Sample_contact_institute | Heinrich-Heine Universität Düsseldorf
| | Sample_contact_address | Universitätsstraße 1
| | Sample_contact_city | Düsseldorf
| | Sample_contact_zip/postal_code | 40225
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM174nnn/GSM174698/suppl/GSM174698.CEL.gz
| | Sample_series_id | GSE7291
| | Sample_series_id | GSE7322
| | Sample_data_row_count | 8793
| | |
|
| |
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