|
| Status |
Public on Oct 15, 2015 |
| Title |
queiscent fibroblast 2 |
| Sample type |
SRA |
| |
|
| Source name |
normal foreskin fibroblast
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: queiscent fibroblast
source: foreskin 2DD
|
| Treatment protocol |
0.5% FBS (Quiescence); 500nM Rapamycin 5 days
|
| Growth protocol |
10 % FBS DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
MP24 Fast Prep green kit
polyA purified mRNAs
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
TOPHAT/CUFFLINK 2.0 was used with parameters --bowtie1 -p 8 -r 20 --solexa-quals --coverage-search --microexon-search--library-type fr-unstranded
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the Seqmonk tool http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each of six samples
|
| |
|
| Submission date |
Jan 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher H. Eskiw |
| E-mail(s) |
c.eskiw@usask.ca
|
| Phone |
306-966-2454
|
| Organization name |
University of Saskatchewan
|
| Department |
Food and Bioproduct Science
|
| Lab |
Eskiw Lab
|
| Street address |
51 Campus Drive
|
| City |
Saskatoon |
| State/province |
SK |
| ZIP/Postal code |
S7N 5A8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE65145 |
Rapamycin induces chromosome reorganization and increases cytokine production in normal human fibroblasts |
|
| Relations |
| BioSample |
SAMN03289356 |
| SRA |
SRX849319 |
