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Sample GSM2562621 Query DataSets for GSM2562621
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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