Search results for the GEO ID: GSE30868  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM765843 | GPL1261 |
|
Parthenogenetic stem cells sample 1 (PSC_1)
|
Parthenogenetic stem cells (PSCs)
|
strain: C57BL/6
cell type: parthenogenetic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765843
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Parthenogenetic stem cells (PSCs) were obtained from superovulated mice. Oocytes were stimulated with strontium-chloride and allowed to develop into blastocysts for isolating PSC at day 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765843/suppl/GSM765843.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765844 | GPL1261 |
|
Parthenogenetic stem cells sample 2 (PSC_2)
|
Parthenogenetic stem cells (PSCs)
|
strain: C57BL/6
cell type: parthenogenetic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765844
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Parthenogenetic stem cells (PSCs) were obtained from superovulated mice. Oocytes were stimulated with strontium-chloride and allowed to develop into blastocysts for isolating PSC at day 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765844/suppl/GSM765844.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765845 | GPL1261 |
|
Parthenogenetic stem cells sample 3 (PSC_3)
|
Parthenogenetic stem cells (PSCs)
|
strain: C57BL/6
cell type: parthenogenetic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765845
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Parthenogenetic stem cells (PSCs) were obtained from superovulated mice. Oocytes were stimulated with strontium-chloride and allowed to develop into blastocysts for isolating PSC at day 6.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765845/suppl/GSM765845.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765846 | GPL1261 |
|
Embryoid body (EB) assays of parthenogenetic stem cells sample 1 (EB_PSC_1)
|
Embryoid body (EB) assays of parthenogenetic stem cells
|
strain: C57BL/6
cell type: embryoid body parthenogenetic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765846
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Parthenogenetic stem cells (PSCs) were subjected to differentiation in embryoid body (EB) assays and cultured for 15 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765846/suppl/GSM765846.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765847 | GPL1261 |
|
Embryoid body (EB) assays of parthenogenetic stem cells sample 2 (EB_PSC_2)
|
Embryoid body (EB) assays of parthenogenetic stem cells
|
strain: C57BL/6
cell type: embryoid body parthenogenetic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765847
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Parthenogenetic stem cells (PSCs) were subjected to differentiation in embryoid body (EB) assays and cultured for 15 days.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765847/suppl/GSM765847.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765848 | GPL1261 |
|
Embryonic stem cells sample 1 (ESC_1)
|
Embryonic stem cells (ESCs)
|
esc line: R1
cell type: embryonic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765848
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Embryonic stem cells (ESCs, line R1) were grown under standard conditions on MEF feeder plus murine leukemia inhibitory factor (LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765848/suppl/GSM765848.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765849 | GPL1261 |
|
Embryonic stem cells sample 2 (ESC_2)
|
Embryonic stem cells (ESCs)
|
esc line: R1
cell type: embryonic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765849
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Embryonic stem cells (ESCs, line R1) were grown under standard conditions on MEF feeder plus murine leukemia inhibitory factor (LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765849/suppl/GSM765849.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
GSM765850 | GPL1261 |
|
Embryonic stem cells sample 3 (ESC_3)
|
Embryonic stem cells (ESCs)
|
esc line: R1
cell type: embryonic stem cells
|
BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).
|
| Sample_geo_accession | GSM765850
| | Sample_status | Public on Feb 23 2013
| | Sample_submission_date | Jul 22 2011
| | Sample_last_update_date | Feb 23 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Embryonic stem cells (ESCs, line R1) were grown under standard conditions on MEF feeder plus murine leukemia inhibitory factor (LIF).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Midi kit (Qiagen, Hilden, Germany) with DNase digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.
| | Sample_hyb_protocol | Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.
| | Sample_scan_protocol | Arrays were scanned using Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Martin,,Zenke
| | Sample_contact_email | Martin.Zenke@rwth-aachen.de
| | Sample_contact_phone | +49-241-80 80760
| | Sample_contact_department | Cell Biology
| | Sample_contact_institute | Institute for Biomedical Engineering
| | Sample_contact_address | Universitatsklinikum Aachen, RWTH
| | Sample_contact_city | Aachen
| | Sample_contact_state | NRW
| | Sample_contact_zip/postal_code | 52074
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM765nnn/GSM765850/suppl/GSM765850.CEL.gz
| | Sample_series_id | GSE30868
| | Sample_data_row_count | 45101
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
