|
| Status |
Public on May 31, 2024 |
| Title |
Batch1_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 |
SAMN19489744 |
| SRA |
SRX11041187 |
