|
| Status |
Public on Nov 24, 2023 |
| Title |
CTCF-del iPSC 2 |
| Sample type |
genomic |
| |
|
| Source name |
iPSC_CTCF_55
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
|
| 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 |
Genomic DNA was isolated with the NucleoSpin Tissue Kit (Macherey-Nagel, Düren, Germany).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard protocols from Illumina
|
| |
|
| Hybridization protocol |
Bisulfite conversion and hybridization to the array was carried out by Life&Brain (Bonn, Germany). Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium EPIC Beadchip using the standard protocol from Illumina.
|
| Scan protocol |
Standard protocols from Illumina
|
| Data processing |
Analysis was performed on RAW idat filed using the R package SeSAMe and the ssNoob normalization. Detection p-values were calculated using the SeSAMe package and the pOOBAH apporach.
|
| |
|
| 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 |
GPL21145 |
| Series (2) |
| GSE247427 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs (methylation) |
| GSE247428 |
CTCF deletion alters the pluripotency and DNA methylation profile of human iPSCs |
|
