|
| Status |
Public on Dec 03, 2019 |
| Title |
Cachectic PDAC, rectus abdominis muscle biopsy 9 |
| Sample type |
RNA |
| |
|
| Source name |
rectus abdominis muscle biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: pancreatic ductal adenocarcinoma
Sex: F
tnm: Stage IV
bw loss in 6 months prior to surgery: 14.6
age: 68
neoadjuvant therapy (y/n): N
survival post-surgery (or days elapsed since surgery, if still alive at time of censor): 73
tissue: rectus abdominis muscle
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies from the rectus abdominis muscle were harvested from patients at the beginning of surgery, and a portion to be used for RNA isolation was immediately snap-frozen in liquid nitrogen followed by storage at -80⁰C. Muscles were minced and homogenized in TRIzol for RNA extraction.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Human Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from rectus abdominis muscle biopsy of cachectic female patient with pancreatic ductal adenocarcinoma.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray hugene20sthsentrezgcdf R package (version 17.0.0).
|
| |
|
| Submission date |
May 01, 2019 |
| Last update date |
Dec 03, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE130563 |
Skeletal Muscle Fibrosis in Pancreatic Cancer Patients with Respect to Survival |
|
