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Sample GSM5351629 Query DataSets for GSM5351629
Status Public on May 31, 2024
Title Batch3_PITX2
Sample type SRA
 
Source name Cell line of human induced pluripotent stem cells (hiPSC)
Organism Homo sapiens
Characteristics tissue: Atrial-like engineered heart tissue (aEHT) derived from hiPSC
group: study sample
genotype: PITX2 Knockout
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from snap frozen aEHT using the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing QC of raw reads using FastQC (v0.11.2)
Trimming read adapters using Trimmomatic (v0.36)
RNA-seq reads were mapped to ENSEMBL Homo_sapiens GRCh38 version 90 using STAR (v2.5.3a)
Read expression was quantified using StringTie (1.3.4d)
A differential expression analysis in R (v4.0.4) using DESeq2 R package (v1.30.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
 
Submission date Jun 01, 2021
Last update date May 31, 2024
Contact name Amer Ghalawinji
E-mail(s) amer.ghalawinji@uni-muenster.de
Organization name WWU
Department Institute of Human Genetics
Lab Department of Genetic Epidemiology
Street address Domagkstrasse 3
City Muenster
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL30173
Series (1)
GSE175944 PITX2 knockout induces key findings of electrical remodeling as seen in persistent atrial fibrillation
Relations
BioSample SAMN19489742
SRA SRX11041189

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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