Search results for the GEO ID: GSE38889  |
(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 |
GSM951538 | GPL1355 |
|
Tumor arising from BDEsp cells rep1
|
Tumor arising from BDEsp cells
|
sample type: BDEsp ICC Tumor
genetic background: Fischer 344
tissue: Intrahepatic cholangiocarcinoma
|
Intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult
|
| Sample_geo_accession | GSM951538
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951538/suppl/GSM951538_AS59.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951539 | GPL1355 |
|
Tumor arising from BDEsp cells rep2
|
Tumor arising from BDEsp cells
|
sample type: BDEsp ICC Tumor
genetic background: Fischer 344
tissue: Intrahepatic cholangiocarcinoma
|
Intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult
|
| Sample_geo_accession | GSM951539
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951539/suppl/GSM951539_AS61.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951540 | GPL1355 |
|
Tumor arising from BDEsp cells rep3
|
Tumor arising from BDEsp cells
|
sample type: BDEsp ICC Tumor
genetic background: Fischer 344
tissue: Intrahepatic cholangiocarcinoma
|
Intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult
|
| Sample_geo_accession | GSM951540
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951540/suppl/GSM951540_AS63.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951541 | GPL1355 |
|
Tumor arising from BDEsp cells rep4
|
Tumor arising from BDEsp cells
|
sample type: BDEsp ICC Tumor
genetic background: Fischer 344
tissue: Intrahepatic cholangiocarcinoma
|
Intrahepatic cholangiocarcinoma from Fischer 344 male rat, young adult
|
| Sample_geo_accession | GSM951541
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951541/suppl/GSM951541_AS65.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951542 | GPL1355 |
|
BDEsp Tumor-Derived Epithelial cells rep1
|
BDEsp Tumor-Derived Epithelial cells
|
sample type: BDEsp Tumor-Derived Epithelial cell line, clone H10 genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Epithelial cell line
|
BDEsp Tumor-Derived Epithelial cell line
|
| Sample_geo_accession | GSM951542
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951542/suppl/GSM951542_AS94.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951543 | GPL1355 |
|
BDEsp Tumor-Derived Epithelial cells rep2
|
BDEsp Tumor-Derived Epithelial cells
|
sample type: BDEsp Tumor-Derived Epithelial cell line, clone H10 genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Epithelial cell line
|
BDEsp Tumor-Derived Epithelial cell line
|
| Sample_geo_accession | GSM951543
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951543/suppl/GSM951543_AS95.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951544 | GPL1355 |
|
BDEsp Tumor-Derived Fibroblastic cells rep1
|
BDEsp Tumor-Derived Fibroblastic cells
|
sample type: BDEsp Tumor-Derived Fibroblastic cell, clone E4
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Fibroblastic cell line
|
BDEsp Tumor-Derived Fibroblastic cell line
|
| Sample_geo_accession | GSM951544
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951544/suppl/GSM951544_AS97.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951545 | GPL1355 |
|
BDEsp Tumor-Derived Fibroblastic cells rep2
|
BDEsp Tumor-Derived Fibroblastic cells
|
sample type: BDEsp Tumor-Derived Fibroblastic cell, clone E4
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Fibroblastic cell line
|
BDEsp Tumor-Derived Fibroblastic cell line
|
| Sample_geo_accession | GSM951545
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951545/suppl/GSM951545_AS98.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951546 | GPL1355 |
|
BDEsp Tumor-Derived Fibroblastic cells rep3
|
BDEsp Tumor-Derived Fibroblastic cells
|
sample type: BDEsp Tumor-Derived Fibroblastic cell, clone E4
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Fibroblastic cell line
|
BDEsp Tumor-Derived Fibroblastic cell line
|
| Sample_geo_accession | GSM951546
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951546/suppl/GSM951546_AS100.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951547 | GPL1355 |
|
BDEsp Tumor-Derived Fibroblastic cells rep4
|
BDEsp Tumor-Derived Fibroblastic cells
|
sample type: BDEsp Tumor-Derived Fibroblastic cell, clone E4
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Fibroblastic cell line
|
BDEsp Tumor-Derived Fibroblastic cell line
|
| Sample_geo_accession | GSM951547
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951547/suppl/GSM951547_AS101.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951548 | GPL1355 |
|
BDEsp Tumor-Derived Epithelial cells rep3
|
BDEsp Tumor-Derived Epithelial cells
|
sample type: BDEsp Tumor-Derived Epithelial cell line, clone H10 genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Epithelial cell line
|
BDEsp Tumor-Derived Epithelial cell line
|
| Sample_geo_accession | GSM951548
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jan 08 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951548/suppl/GSM951548_AS120.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951549 | GPL1355 |
|
BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells
|
BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells
|
sample type: BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells
|
BDEsp Tumor-Derived Epithelial cells in Co-Culture with BDEsp Tumor-Derived Fibroblastic cells
|
| Sample_geo_accession | GSM951549
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951549/suppl/GSM951549_AS123.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
GSM951550 | GPL1355 |
|
BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells
|
BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells
|
sample type: BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells
genetic background: Fischer 344
cell type: BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells
|
BDEsp Tumor-Derived Fibroblastic cells in Co-Culture with BDEsp Tumor-Derived Epithelial cells
|
| Sample_geo_accession | GSM951550
| | Sample_status | Public on Jun 23 2012
| | Sample_submission_date | Jun 22 2012
| | Sample_last_update_date | Jun 23 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | BDEsp tumor-derived cells lines were grown in a rat tail type I collagen gel matrix, alone or in co-culture. For the co-cultures, cholangiocarcinoma (Epithelial) cells were plated at a density of 1 x 105 cells/mL and with a-SMA positive CAF (Fibroblasts) at various plating densities, ranging 0–8 x 105 cells/gel.
| | Sample_growth_protocol_ch1 | Tissues were snap-frozen immediately after extirpation from the animal.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GC3000 scanner.
| | Sample_data_processing | After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries was performed using the log-scale Robust Multiarray Analysis (RMA) method.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Catherine,,Dumur
| | Sample_contact_department | Pathology
| | Sample_contact_institute | VCU
| | Sample_contact_address | 403 North 13th
| | Sample_contact_city | Richmond
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 23233
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM951nnn/GSM951550/suppl/GSM951550_AS126.CEL.gz
| | Sample_series_id | GSE38889
| | Sample_data_row_count | 31099
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
