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Sample GSM862505 Query DataSets for GSM862505
Status Public on Jun 07, 2012
Title PDCCETumor_FreshFrozen_CRC170X2A
Sample type RNA
 
Source name mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: lung
Treatment protocol N/A
Growth protocol 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.
Extracted molecule total RNA
Extraction protocol 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).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization 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).
Scan protocol GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
Data processing The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
 
Submission date Jan 17, 2012
Last update date Jun 07, 2012
Contact name David Hsu
Organization name Duke University
Department Medical Oncology
Street address 905 S. LaSalle St. Rm 3008
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL570
Series (1)
GSE35144 Molecular Evaluation of Patient-Derived Colorectal Cancer Explants as a Pre-clinical Mouse Model of Colorectal Cancer

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA signal.

Data table
ID_REF VALUE
1007_s_at 11.94314175
1053_at 8.1408262
117_at 7.475543394
121_at 9.879986241
1255_g_at 5.421500383
1294_at 8.693706913
1316_at 7.12881661
1320_at 6.332240316
1405_i_at 4.784064755
1431_at 6.34666313
1438_at 11.0279725
1487_at 9.251531956
1494_f_at 7.904804545
1552256_a_at 9.775782038
1552257_a_at 8.839235577
1552258_at 6.752152964
1552261_at 7.836104905
1552263_at 6.340624838
1552264_a_at 7.663232987
1552266_at 6.842831291

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM862505.CEL.gz 5.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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