|
| Status |
Public on Jun 18, 2014 |
| Title |
Normal Fibroblast (NF) [RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Normal Fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed (C57BL/6 and BALB/c)
genotype/variation: tf1acre-;KrasWT;Tgfrb2flox/flox
tissue: normal pancreas
cell type: Normal Fibroblast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard SOLiD protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Applied Biosystems LifeScope software was used for basecalling.
Sequenced reads were mapped to mm10 genome using the default LifeScope RNA-Seq parameters.
DESeq (Anders & Huber, 2010) was used for assessment of transcript abundance measurements and doing differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcript abundance measurements for each sample. The 'CAF90vsNF1493.xls' file contains expression fold change values.
|
| |
|
| Submission date |
Mar 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Valerie LeBleu |
| E-mail(s) |
vlebleumdaprofessional@gmail.com
|
| Organization name |
MDACC
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL15907 |
| Series (2) |
| GSE55870 |
Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) [RNA-seq] |
| GSE55871 |
Gene Expression Analysis of Cancer-Associated Fibroblast (CAF) compared to Normal Fibroblast (NF) |
|
| Relations |
| BioSample |
SAMN02688799 |
| SRA |
SRX488254 |
