|
| Status |
Public on Nov 22, 2017 |
| Title |
Pa033ST |
| Sample type |
SRA |
| |
|
| Source name |
right atrial appendage biopsies
|
| Organism |
Homo sapiens |
| Characteristics |
race: Indian
gender: female
cell type: Cardiac fibroblasts
treatment: human recombinant TGFB1 (Serotec)
|
| Treatment protocol |
Cardiac fibroblasts were cultured in serum-free media for 24 hours prior to treatment. They were further treated with TGFB1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were constructed with TruSeq Stranded mRNA Library Prep kit (Illumina) using 0.8µg of total RNA. RNA-seq, barcoded libraries were multiplexed and sequenced as paired-end reads on Illumina HiSeq 2500 platform using NextSeq High output 150 cycles kit across 4 lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Alignment: High-quality reads were mapped to Ensembl human GRCh38 v78 reference genome using TopHat v2.0.12 with the following parameters: prefilter multihits, mate inner distance of 0 and read realign edit distance of 0 (default was used for the rest of parameters).
Gene level counts were computed by using HTSeq (version 0.6.1)
Genome_build: GRCh38 v78
Supplementary_files_format_and_content: 168_fibroblast_samples_gene_counts.txt : file with gene level counts, fibroblasts_samples_info.txt: technical, clinical covariates and samples treatment
|
| |
|
| Submission date |
Apr 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sonia Chothani |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke-NUS school of medicine
|
| Lab |
Prof. Stuart Cook
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE97117 |
Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis |
| GSE97358 |
Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [168 human cardiac fibroblasts] |
|
| Relations |
| BioSample |
SAMN06678148 |
| SRA |
SRX2701847 |
