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Status |
Public on Dec 03, 2019 |
Title |
Non-cancer control, rectus abdominis muscle biopsy 15 |
Sample type |
RNA |
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Source name |
rectus abdominis muscle biopsy
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Organism |
Homo sapiens |
Characteristics |
diagnosis: choledochal cyst Sex: F tnm: n/a bw loss in 6 months prior to surgery: 11.1 age: 60 neoadjuvant therapy (y/n): n/a survival post-surgery (or days elapsed since surgery, if still alive at time of censor): n.d. (not determined) tissue: rectus abdominis muscle
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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.
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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.
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Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
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Description |
Gene expression data from rectus abdominis muscle biopsy of female non-cancer control with choledochal cyst.
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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).
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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 |
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