|
| Status |
Public on Nov 24, 2023 |
| Title |
CTCF-del, 55 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPSC
chip antibody: CTCF (Active Motif, #61311)
|
| 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 |
genomic DNA |
| Extraction protocol |
iPSCs were fixed with 1% formaldehyde and fractionated using the Covaris M220 using Peak power 75W, Duty factor 5%, Cycle/burst 200 at 6 degrees for 25 minutes to obtain chromatin fractions Immunoprecipitation was performed with the CTCF antibody using the ChIP-IT Express Chromatin Immunoprecipitation Kit (Activ Motiff) using standard protocols.
Illumina TruSeq Nano DNA Library Prep Kit, standard library preparation protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The Nextflow nf-core/chipseq pipeline (v2.0.0; https://doi.org/10.5281/zenodo.7139814) was used for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data together with Singularity containers
Assembly: GRCh38
Supplementary files format and content: narrowPeak files that provides called peaks of signal enrichment based on pooled, normalized data.
|
| |
|
| 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) |
| GSE247425 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (ChIP-Seq) |
| GSE247428 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs |
|
| Relations |
| BioSample |
SAMN38194207 |
| SRA |
SRX22478081 |
