Search results for the GEO ID: GSE38121  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM935083 | GPL570 |
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HCC 827
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HCC 827
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cell line: HCC 827
tissue: Lung
erlotinib resistance: No
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Gene expression data from the parental cell line, HCC827
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| Sample_geo_accession | GSM935083
| | Sample_status | Public on Jun 16 2012
| | Sample_submission_date | May 22 2012
| | Sample_last_update_date | Jun 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Growth media was treated with drug (Erlotinib), which was dissolved in 10 mM concentrate (1000x), or vehicle control (DMSO only).
| | Sample_growth_protocol_ch1 | Grown and subcultured as according to ATCC protocol for HCC827
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's RNeasy kit was used according to the manufacturer's instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1-2 μg of total RNA were depleted of ribosomal RNA, (Ribominus Eukaryote kit, Invitrogen). Efficiency of the depletion was checked on BioAnalyzer. Resulting material was labeled using the Affymetrix WT Sense Target Labeling Assay (Affymetrix).
| | Sample_hyb_protocol | 5.5 μg of single stranded cDNA was fragmented, labeled and hybridized to the Affymetrix array for 16 hours. Post hybridization staining and washing was performed according to the manufacturer’s instructions (Affymetrix).
| | Sample_scan_protocol | chips were scanned with a high-numerical Aperture and flying objective (FOL) lens in the GS3000 scanner (Affymetrix). Images were quantified using GCOS 1.4 (GeneChip Operating Software, Affymetrix).
| | Sample_data_processing | Raw CEL files were processed with Aroma Affymetrix (Bengtsson et al., 2008) using standard RMA background adjustment and quantile normalization. Summarization was fit to both exons and RefSeq transcripts using the HuEx-1_0-st-v2,main,A20071112,EP CDF annotation. Additionally, outlier profiles for all transcripts and outlier assignments in all tumors were determined from normalized expression data as detailed in Experimental Procedures and as previously described (Ghosh and Chinnaiyan, 2009).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Elton,,Chan
| | Sample_contact_email | echan@medicine.ucsf.edu
| | Sample_contact_department | Medicine
| | Sample_contact_institute | UCSF
| | Sample_contact_address | 600 16th Street Rm N216R
| | Sample_contact_city | San Francisco
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 94158
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM935nnn/GSM935083/suppl/GSM935083.CEL.gz
| | Sample_series_id | GSE38121
| | Sample_data_row_count | 43946
| | |
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GSM935084 | GPL570 |
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HCC 827 ER1
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HCC827 ER1
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cell line: HCC 827
tissue: Lung
erlotinib resistance: Yes
|
Gene expression data from the Erlotinib-resistant cell line, HCC827 ER1
|
| Sample_geo_accession | GSM935084
| | Sample_status | Public on Jun 16 2012
| | Sample_submission_date | May 22 2012
| | Sample_last_update_date | Jun 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Growth media was treated with drug (Erlotinib), which was dissolved in 10 mM concentrate (1000x), or vehicle control (DMSO only).
| | Sample_growth_protocol_ch1 | Grown and subcultured as according to ATCC protocol for HCC827
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's RNeasy kit was used according to the manufacturer's instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1-2 μg of total RNA were depleted of ribosomal RNA, (Ribominus Eukaryote kit, Invitrogen). Efficiency of the depletion was checked on BioAnalyzer. Resulting material was labeled using the Affymetrix WT Sense Target Labeling Assay (Affymetrix).
| | Sample_hyb_protocol | 5.5 μg of single stranded cDNA was fragmented, labeled and hybridized to the Affymetrix array for 16 hours. Post hybridization staining and washing was performed according to the manufacturer’s instructions (Affymetrix).
| | Sample_scan_protocol | chips were scanned with a high-numerical Aperture and flying objective (FOL) lens in the GS3000 scanner (Affymetrix). Images were quantified using GCOS 1.4 (GeneChip Operating Software, Affymetrix).
| | Sample_data_processing | Raw CEL files were processed with Aroma Affymetrix (Bengtsson et al., 2008) using standard RMA background adjustment and quantile normalization. Summarization was fit to both exons and RefSeq transcripts using the HuEx-1_0-st-v2,main,A20071112,EP CDF annotation. Additionally, outlier profiles for all transcripts and outlier assignments in all tumors were determined from normalized expression data as detailed in Experimental Procedures and as previously described (Ghosh and Chinnaiyan, 2009).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Elton,,Chan
| | Sample_contact_email | echan@medicine.ucsf.edu
| | Sample_contact_department | Medicine
| | Sample_contact_institute | UCSF
| | Sample_contact_address | 600 16th Street Rm N216R
| | Sample_contact_city | San Francisco
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 94158
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM935nnn/GSM935084/suppl/GSM935084.CEL.gz
| | Sample_series_id | GSE38121
| | Sample_data_row_count | 43946
| | |
|
GSM935085 | GPL570 |
|
HCC 827 ER2
|
HCC827 ER2
|
cell line: HCC 827
tissue: Lung
erlotinib resistance: Yes
|
Gene expression data from the Erlotinib-resistant cell line, HCC827 ER2
|
| Sample_geo_accession | GSM935085
| | Sample_status | Public on Jun 16 2012
| | Sample_submission_date | May 22 2012
| | Sample_last_update_date | Jun 16 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Growth media was treated with drug (Erlotinib), which was dissolved in 10 mM concentrate (1000x), or vehicle control (DMSO only).
| | Sample_growth_protocol_ch1 | Grown and subcultured as according to ATCC protocol for HCC827
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's RNeasy kit was used according to the manufacturer's instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1-2 μg of total RNA were depleted of ribosomal RNA, (Ribominus Eukaryote kit, Invitrogen). Efficiency of the depletion was checked on BioAnalyzer. Resulting material was labeled using the Affymetrix WT Sense Target Labeling Assay (Affymetrix).
| | Sample_hyb_protocol | 5.5 μg of single stranded cDNA was fragmented, labeled and hybridized to the Affymetrix array for 16 hours. Post hybridization staining and washing was performed according to the manufacturer’s instructions (Affymetrix).
| | Sample_scan_protocol | chips were scanned with a high-numerical Aperture and flying objective (FOL) lens in the GS3000 scanner (Affymetrix). Images were quantified using GCOS 1.4 (GeneChip Operating Software, Affymetrix).
| | Sample_data_processing | Raw CEL files were processed with Aroma Affymetrix (Bengtsson et al., 2008) using standard RMA background adjustment and quantile normalization. Summarization was fit to both exons and RefSeq transcripts using the HuEx-1_0-st-v2,main,A20071112,EP CDF annotation. Additionally, outlier profiles for all transcripts and outlier assignments in all tumors were determined from normalized expression data as detailed in Experimental Procedures and as previously described (Ghosh and Chinnaiyan, 2009).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Elton,,Chan
| | Sample_contact_email | echan@medicine.ucsf.edu
| | Sample_contact_department | Medicine
| | Sample_contact_institute | UCSF
| | Sample_contact_address | 600 16th Street Rm N216R
| | Sample_contact_city | San Francisco
| | Sample_contact_state | California
| | Sample_contact_zip/postal_code | 94158
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM935nnn/GSM935085/suppl/GSM935085.CEL.gz
| | Sample_series_id | GSE38121
| | Sample_data_row_count | 43946
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