Search results for the GEO ID: GSE48397  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1177015 | GPL1261 |
|
lung fibroblasts, biological replicate 1
|
lung fibroblasts
|
tissue: lung
cell type: normal fibroblasts
|
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs561
|
| Sample_geo_accession | GSM1177015
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177015/suppl/GSM1177015_Silvestre_LFs_vs561_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177015/suppl/GSM1177015_Silvestre_LFs_vs561_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177016 | GPL1261 |
|
lung fibroblasts, biological replicate 2
|
lung fibroblasts
|
tissue: lung
cell type: normal fibroblasts
|
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs585
|
| Sample_geo_accession | GSM1177016
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177016/suppl/GSM1177016_Silvestre_LFs_vs585_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177016/suppl/GSM1177016_Silvestre_LFs_vs585_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177017 | GPL1261 |
|
lung fibroblasts, biological replicate 3
|
lung fibroblasts
|
tissue: lung
cell type: normal fibroblasts
|
Gene expression data from lung fibroblasts, biological replicate 1
LFs vs686
|
| Sample_geo_accession | GSM1177017
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177017/suppl/GSM1177017_Silvestre_LFs_vs686_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177017/suppl/GSM1177017_Silvestre_LFs_vs686_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177018 | GPL1261 |
|
lung fibroblasts, biological replicate 4
|
lung fibroblasts
|
tissue: lung
cell type: normal fibroblasts
|
Gene expression data from lung fibroblasts, biological replicate 1
LFs ls934
|
| Sample_geo_accession | GSM1177018
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177018/suppl/GSM1177018_Silvestre_LFs_Is934_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177018/suppl/GSM1177018_Silvestre_LFs_Is934_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177019 | GPL1261 |
|
lung fibroblasts, biological replicate 5
|
lung fibroblasts
|
tissue: lung
cell type: normal fibroblasts
|
Gene expression data from lung fibroblasts, biological replicate 1
LFs ls938
|
| Sample_geo_accession | GSM1177019
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177019/suppl/GSM1177019_Silvestre_LFs_Is938_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177019/suppl/GSM1177019_Silvestre_LFs_Is938_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177020 | GPL1261 |
|
carcinoma-asssociated fibroblasts, biological replicate 1
|
carcinoma-asssociated fibroblasts
|
tissue: lung
cell type: carcinoma-asssociated fibroblasts
|
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls930
|
| Sample_geo_accession | GSM1177020
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177020/suppl/GSM1177020_Silvestre_CAFs_Is930_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177020/suppl/GSM1177020_Silvestre_CAFs_Is930_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177021 | GPL1261 |
|
carcinoma-asssociated fibroblasts, biological replicate 2
|
carcinoma-asssociated fibroblasts
|
tissue: lung
cell type: carcinoma-asssociated fibroblasts
|
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls940
|
| Sample_geo_accession | GSM1177021
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177021/suppl/GSM1177021_Silvestre_CAFs_Is940_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177021/suppl/GSM1177021_Silvestre_CAFs_Is940_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177022 | GPL1261 |
|
carcinoma-asssociated fibroblasts, biological replicate 3
|
carcinoma-asssociated fibroblasts
|
tissue: lung
cell type: carcinoma-asssociated fibroblasts
|
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls953
|
| Sample_geo_accession | GSM1177022
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177022/suppl/GSM1177022_Silvestre_CAFs_Is953_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177022/suppl/GSM1177022_Silvestre_CAFs_Is953_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177023 | GPL1261 |
|
carcinoma-asssociated fibroblasts, biological replicate 4
|
carcinoma-asssociated fibroblasts
|
tissue: lung
cell type: carcinoma-asssociated fibroblasts
|
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls955
|
| Sample_geo_accession | GSM1177023
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177023/suppl/GSM1177023_Silvestre_CAFs_Is955_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177023/suppl/GSM1177023_Silvestre_CAFs_Is955_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
| | |
|
GSM1177024 | GPL1261 |
|
carcinoma-asssociated fibroblasts, biological replicate 5
|
carcinoma-asssociated fibroblasts
|
tissue: lung
cell type: carcinoma-asssociated fibroblasts
|
Gene expression data from carcinoma-asssociated fibroblasts, biological replicate 1
CAFs ls990
|
| Sample_geo_accession | GSM1177024
| | Sample_status | Public on Jul 10 2013
| | Sample_submission_date | Jun 28 2013
| | Sample_last_update_date | Jul 10 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | LFs and CAFs were trypsinized and plated at 10X6 cells/10cm dish, and grown overnight in 10% serum DMEM (including antibiotics).
| | Sample_growth_protocol_ch1 | LFs and CAFs were grown in 10% serum DMEM (including antibiotics) after isolation from mouse lungs and expanded for 10-14 days before being plated for RNA collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up using Qiagen on-column Dnase treatment
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | cDNA synthesis, biotinylation of cRNA and hybridization to mouse Genechip 430A v2 containing 39,000 probes was performed according to the manufacturer’s instructions (Affymetrix, Santa Clara).
| | Sample_scan_protocol | GeneChips were scanned using Affymetrix scanner
| | Sample_data_processing | The data were analyzed with RMA using Affymetrix default analysis settings using Expression Console. On the RMA normalized data statistical test LIMMA is performed for D.E
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Dedeepya,,Vaka
| | Sample_contact_email | dvaka@stanford.edu
| | Sample_contact_laboratory | Alejandro Sweet-Cordero
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Stanford
| | Sample_contact_address | 265 Campus Drive
| | Sample_contact_city | Palo Alto
| | Sample_contact_zip/postal_code | 94035
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177024/suppl/GSM1177024_Silvestre_CAFs_Is990_Mouse430_2.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1177nnn/GSM1177024/suppl/GSM1177024_Silvestre_CAFs_Is990_Mouse430_2.rma.chp.gz
| | Sample_series_id | GSE48397
| | Sample_data_row_count | 45101
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