|
| Status |
Public on Nov 24, 2023 |
| Title |
iPSC, CTCF-del, 55 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPSC
genotype: CTCF-del
|
| Treatment protocol |
CRISPR-cas 9 mediated CTCF deletion. Transfection of complexed crRNA-tracrRNA and Cas9 using the NEON transfection system using standard protocols.
|
| Growth protocol |
iPSCs were cultured on tissue culture plastic coated with vitronectin in StemMACS iPS-Brew XF
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Library preparation was carried out using QuantSeq 3ยด-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GLP26351
|
| Data processing |
Quality of FASTQ files was quantified using FastQC, and adaptor sequences and low-quality reads were trimmed using Trim Galore. Alignment of the reads was done using STAR (hg38 genome build) and transcript quantification was performed using Salmon. The resulting count matrices were normalized by size factor and dispersion using the DESeq2 package in R (Love et al., 2014)
Assembly: GRCh38
Supplementary files format and content: .sf files is a salmon transcript abundance estimation file
|
| |
|
| Submission date |
Nov 09, 2023 |
| Last update date |
Nov 24, 2023 |
| Contact name |
Wolfgang Wagner |
| E-mail(s) |
wwagner@ukaachen.de
|
| Phone |
+49 241 8088611
|
| Organization name |
RWTH Aachen University
|
| Department |
Helmholtz Institute for Biomedical Engineering
|
| Lab |
Stem Cell Biology and Cellular Engineering
|
| Street address |
Pauwelsstrasse 20
|
| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE247426 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (RNA-Seq) |
| GSE247428 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs |
|
| Relations |
| BioSample |
SAMN38194216 |
| SRA |
SRX22477949 |
