Search results for the GEO ID: GSE35144  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM862441 | GPL570 |
|
HumanTumor_FreshFrozen_CRC028A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862441
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862441/suppl/GSM862441.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862442 | GPL570 |
|
HumanTumor_FreshFrozen_CRC039A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862442
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862442/suppl/GSM862442.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862443 | GPL570 |
|
HumanTumor_FreshFrozen_CRC057A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862443
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862443/suppl/GSM862443.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862444 | GPL570 |
|
HumanTumor_FreshFrozen_CRC020
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862444
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862444/suppl/GSM862444.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862445 | GPL570 |
|
HumanTumor_FreshFrozen_CRC034
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862445
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862445/suppl/GSM862445.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862446 | GPL570 |
|
HumanTumor_FreshFrozen_CRC075A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862446
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862446/suppl/GSM862446.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862447 | GPL570 |
|
HumanTumor_FreshFrozen_CRC102A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862447
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862447/suppl/GSM862447.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862448 | GPL570 |
|
HumanTumor_FreshFrozen_CRC119A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862448
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862448/suppl/GSM862448.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862449 | GPL570 |
|
HumanTumor_FreshFrozen_CRC040
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862449
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862449/suppl/GSM862449.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862450 | GPL570 |
|
HumanTumor_FreshFrozen_CRC105B
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862450
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862450/suppl/GSM862450.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862451 | GPL570 |
|
HumanTumor_FreshFrozen_CRC170
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862451
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862451/suppl/GSM862451.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862453 | GPL570 |
|
HumanTumor_FreshFrozen_CRC167
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862453
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862453/suppl/GSM862453.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862454 | GPL570 |
|
HumanTumor_FreshFrozen_CRC054
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862454
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862454/suppl/GSM862454.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862455 | GPL570 |
|
HumanTumor_FreshFrozen_CRC120A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: omentum
|
|
| Sample_geo_accession | GSM862455
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862455/suppl/GSM862455.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862456 | GPL570 |
|
HumanTumor_FreshFrozen_CRC030A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862456
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862456/suppl/GSM862456.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862457 | GPL570 |
|
HumanTumor_FreshFrozen_CRC066A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862457
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862457/suppl/GSM862457.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862458 | GPL570 |
|
HumanTumor_FreshFrozen_CRC083A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: peritoneal
|
|
| Sample_geo_accession | GSM862458
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862458/suppl/GSM862458.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862459 | GPL570 |
|
HumanTumor_FreshFrozen_CRC025
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862459
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862459/suppl/GSM862459.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862460 | GPL570 |
|
HumanTumor_FreshFrozen_CRC096
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862460
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862460/suppl/GSM862460.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862461 | GPL570 |
|
HumanTumor_FreshFrozen_CRC103
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862461
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862461/suppl/GSM862461.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862462 | GPL570 |
|
HumanTumor_FreshFrozen_CRC108
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862462
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862462/suppl/GSM862462.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862463 | GPL570 |
|
HumanTumor_FreshFrozen_CRC093A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862463
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862463/suppl/GSM862463.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862464 | GPL570 |
|
HumanTumor_FreshFrozen_CRC133A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862464
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862464/suppl/GSM862464.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862465 | GPL570 |
|
HumanTumor_FreshFrozen_CRC043A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862465
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862465/suppl/GSM862465.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862466 | GPL570 |
|
HumanTumor_FreshFrozen_CRC159
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862466
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862466/suppl/GSM862466.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862467 | GPL570 |
|
HumanTumor_FreshFrozen_CRC149A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862467
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862467/suppl/GSM862467.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862468 | GPL570 |
|
HumanTumor_FreshFrozen_CRC162A
|
human tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: patient tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862468
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862468/suppl/GSM862468.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862469 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC105X11A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862469
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862469/suppl/GSM862469.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862470 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC028XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862470
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862470/suppl/GSM862470.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862471 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC039XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862471
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862471/suppl/GSM862471.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862472 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC020XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862472
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862472/suppl/GSM862472.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862473 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC025XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862473
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862473/suppl/GSM862473.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862474 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC034XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862474
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862474/suppl/GSM862474.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862475 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC054XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862475
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862475/suppl/GSM862475.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862476 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC075XB
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862476
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862476/suppl/GSM862476.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862477 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC102XA
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862477
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862477/suppl/GSM862477.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862478 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC057XC
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862478
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862478/suppl/GSM862478.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862479 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC105XB
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862479
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862479/suppl/GSM862479.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862480 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC167X
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862480
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862480/suppl/GSM862480.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862481 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC025X2A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862481
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862481/suppl/GSM862481.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862482 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC030X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862482
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862482/suppl/GSM862482.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862483 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC040X5A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862483
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862483/suppl/GSM862483.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862484 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC030X5A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: colorectal
|
|
| Sample_geo_accession | GSM862484
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862484/suppl/GSM862484.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862485 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC083X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: peritoneal
|
|
| Sample_geo_accession | GSM862485
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862485/suppl/GSM862485.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862486 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC093X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862486
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862486/suppl/GSM862486.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862487 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC096X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862487
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862487/suppl/GSM862487.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862488 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC103X4A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862488
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862488/suppl/GSM862488.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862489 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC108X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862489
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862489/suppl/GSM862489.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862490 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC119X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862490
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862490/suppl/GSM862490.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862491 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC120X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: omentum
|
|
| Sample_geo_accession | GSM862491
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862491/suppl/GSM862491.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862492 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC096X14A3
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862492
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862492/suppl/GSM862492.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862493 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC066X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862493
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862493/suppl/GSM862493.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862494 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC103X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862494
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862494/suppl/GSM862494.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862495 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC170X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862495
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862495/suppl/GSM862495.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862496 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC167X3A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862496
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862496/suppl/GSM862496.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862497 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC167X1B
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862497
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862497/suppl/GSM862497.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862499 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC133X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862499
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862499/suppl/GSM862499.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862500 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC133X7A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862500
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862500/suppl/GSM862500.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862501 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC149X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862501
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862501/suppl/GSM862501.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862502 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC149X5A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862502
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862502/suppl/GSM862502.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862503 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC159X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862503
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862503/suppl/GSM862503.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862504 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC162X1A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: liver
|
|
| Sample_geo_accession | GSM862504
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862504/suppl/GSM862504.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
GSM862505 | GPL570 |
|
PDCCETumor_FreshFrozen_CRC170X2A
|
mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
|
primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: lung
|
|
| Sample_geo_accession | GSM862505
| | Sample_status | Public on Jun 07 2012
| | Sample_submission_date | Jan 17 2012
| | Sample_last_update_date | Jun 07 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | N/A
| | Sample_growth_protocol_ch1 | Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
| | Sample_scan_protocol | GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Shiaowen,,Hsu
| | Sample_contact_department | Institute for Genome Sciences and Policy
| | Sample_contact_institute | Duke University
| | Sample_contact_address | 101 Science Dr, room 2323
| | Sample_contact_city | Durham
| | Sample_contact_state | NC
| | Sample_contact_zip/postal_code | 27713
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM862nnn/GSM862505/suppl/GSM862505.CEL.gz
| | Sample_series_id | GSE35144
| | Sample_data_row_count | 54675
| | |
|
| |
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