|
| Status |
Public on May 01, 2019 |
| Title |
shCtrl-1: Cancer associated fibroblasts expressing shCtrl construct, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
CAFs expressing shCtrl construct
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Cancer associated fibroblasts (CAFs)
expression construct: shCtrl
|
| Treatment protocol |
All cell lines were stably infected with the indicated constructs and no additional treatment was performed.
|
| Growth protocol |
All cell lines were grown in methionine-free DMEM supplemented with 10% dialyzed fetal bovine serum and 10 micromolar methionine for 21 days before collection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Qiagen AllPrep DNA/RNA Mini Kit per manufacturer's instructions. RNA integrity was checked on a bioanalyzer (Agilent,Inc). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis
|
| Label |
biotin
|
| Label protocol |
700 pg of total RNA was used to generate double strand cDNA and the Ds cDNA was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher Scientific, Inc).
|
| |
|
| Hybridization protocol |
5.5 ug of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher Scientific, Inc).
|
| Scan protocol |
The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc)
|
| Description |
Gene expression data from human CAFs expressing shCtrl construct, biological replicate 1
|
| Data processing |
Transcriptome Analysis Software 4.0 (TAS 4.0) Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA)
|
| |
|
| Submission date |
Mar 29, 2018 |
| Last update date |
May 01, 2019 |
| Contact name |
Mark Adam Eckert |
| E-mail(s) |
meckert@bsd.uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
OB/GYN
|
| Lab |
Lengyel Lab
|
| Street address |
929 East 57th St, W107
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE112497 |
Microarray analysis of NNMT overexpression and knockdown in stromal cells |
|
