|
Status |
Public on Nov 22, 2017 |
Title |
Pa066BS |
Sample type |
SRA |
|
|
Source name |
right atrial appendage biopsies
|
Organism |
Homo sapiens |
Characteristics |
race: Chinese gender: female cell type: Cardiac fibroblasts treatment: Control
|
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 |
SAMN06678178 |
SRA |
SRX2701908 |