Search results for the GEO ID: GSE14054  |
(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 |
GSM352580 | GPL570 |
|
HeLa_ctrlsiRNA_totalRNA_replicate1
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352580
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352580/suppl/GSM352580.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352580/suppl/GSM352580.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352582 | GPL570 |
|
HeLa_ctrlsiRNA_totalRNA_replicate2
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352582
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352582/suppl/GSM352582.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352582/suppl/GSM352582.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352587 | GPL570 |
|
HeLa_Imp8siRNA_totalRNA_replicate2
|
HeLa cells, Importin8 siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352587
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352587/suppl/GSM352587.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352587/suppl/GSM352587.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352588 | GPL570 |
|
HeLa_TNRC6BsiRNA_totalRNA_replicate1
|
HeLa cells, TNRC6B siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352588
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352588/suppl/GSM352588.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352588/suppl/GSM352588.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352589 | GPL570 |
|
HeLa_TNRC6BsiRNA_totalRNA_replicate2
|
HeLa cells, TNRC6B siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352589
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA for microarray analysis was isolated using PrepEase Kit for total RNA (USB, USA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352589/suppl/GSM352589.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352589/suppl/GSM352589.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352590 | GPL570 |
|
HeLa_ctrlsiRNA_IPedRNA_replicate1
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352590
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352590/suppl/GSM352590.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352590/suppl/GSM352590.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352621 | GPL570 |
|
HeLa_ctrlsiRNA_IPedRNA_replicate2
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352621
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352621/suppl/GSM352621.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352621/suppl/GSM352621.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352622 | GPL570 |
|
HeLa_ctrlsiRNA_IPedRNA_replicate3
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352622
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352622/suppl/GSM352622.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352622/suppl/GSM352622.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352628 | GPL570 |
|
HeLa_ctrlsiRNA_IPedRNA_replicate4
|
HeLa cells, control siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352628
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352628/suppl/GSM352628.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352628/suppl/GSM352628.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352629 | GPL570 |
|
HeLa_Imp8siRNA_IPedRNA_replicate1
|
HeLa cells, Importin8 siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352629
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352629/suppl/GSM352629.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352629/suppl/GSM352629.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352630 | GPL570 |
|
HeLa_Imp8siRNA_IPedRNA_replicate2
|
HeLa cells, Importin8 siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352630
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352630/suppl/GSM352630.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352630/suppl/GSM352630.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352675 | GPL570 |
|
HeLa_Imp8siRNA_IPedRNA_replicate3
|
HeLa cells, Importin8 siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352675
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352675/suppl/GSM352675.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352675/suppl/GSM352675.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
GSM352676 | GPL570 |
|
HeLa_Imp8siRNA_IPedRNA_replicate4
|
HeLa cells, Importin8 siRNA transfected
|
HeLa S3 cells
|
Sample processing for hybridization was performed as described in the GeneChip® Expression Analysis Technical Manual.
|
| Sample_geo_accession | GSM352676
| | Sample_status | Public on Jan 22 2009
| | Sample_submission_date | Dec 19 2008
| | Sample_last_update_date | Jan 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | HeLa S3 cells were reverse transfected in 10 cm plates with 40 nM siRNAs and Lipofectamine RNAiMAX for 4 days.
| | Sample_growth_protocol_ch1 | HeLa S3 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin. Cells were cultivated at 37°C in atmosphere with 5% CO2. Cells were routinely passaged at 70% confluency.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | To analyze mRNA binding to endogenous Ago2, siRNA-transfected cells were harvested 4d post transfection and lysed in lysis buffer (150 mM KCl/25 mM Tris-HCl pH 7.5/2 mM EDTA/1mM NaF/0.5% NP-40/0.5 mM DTT/0.5 mM AEBSF/Ribolock, Fermentas, 1μl per ml of buffer). Lysates were cleared by centrifugation and incubated with anti-Ago2 protein G sepharose beads for 3 h at 4°C. Immunoprecipitates were washed three times with IP wash buffer (300 mM NaCl/50 mM Tris pH 7.5/1mM NaF, 0.01% NP-40/5 mM MgCl2) and once with PBS. IP samples were proteinase K-digested, followed by phenol/chloroform/isopropyl alcohol extraction and precipitation of RNA in 80% ethanol at -20°C. RNA was pelleted, dried and treated with DNaseI (Fermentas) for 30 min at 37°C, followed by thermal inactivation of DNaseI.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Samples were labeled according to the GeneChip® Expression Analysis Technical Manual (Affymetrix), using the two-cycle cDNA synthesis protocol.
| | Sample_hyb_protocol | Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays according to the GeneChip® Expression Analysis Technical Manual (Affymetrix).
| | Sample_scan_protocol | Scanning was performed as described in the GeneChip® Expression Analysis Technical Manual.
| | Sample_data_processing | Microarray data were analyzed using Agilent Genespring software. Expression values below 0.01 were set to 0.01. Each measurement was divided by the 50th percentile of all measurements in that sample.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Gunter,,Meister
| | Sample_contact_email | meister@biochem.mpg.de
| | Sample_contact_laboratory | RNA Biology
| | Sample_contact_department | Center for Integrated Protein Science Munich (CIPSM)
| | Sample_contact_institute | Max Planck Institute of Biochemistry
| | Sample_contact_address | Am Klopferspitz 18
| | Sample_contact_city | Martinsried
| | Sample_contact_zip/postal_code | 82152
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352676/suppl/GSM352676.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM352nnn/GSM352676/suppl/GSM352676.CHP.gz
| | Sample_series_id | GSE14054
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
