|
| Status |
Public on Mar 11, 2024 |
| Title |
ChIPseq_ESC_CTCF_IP_wt_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cells
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
genotype: wild-type
antibody: CTCF
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using AMPure XP beads
Sequencing libraries were prepared using the NEBNext Ultra Library Preparation Kit (NEB) with 12 PCR amplification cycles for Ips and 5 PCR amplification cycles for inputs.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. Reads were mapped to mm10 using QuasR (Gaidatzis et al, Bioinformatics 2015) with default parameters, allowing only for uniquely mapping reads.
wig files were generated using the qExportWig function from the QuasR package with scaling=1e6 . The scores in the wig file represent the number of fragment midpoints per 100bp window and per million reads in the library.
Assembly: mm10
Supplementary files format and content: wig
|
| |
|
| Submission date |
Jun 06, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE234273 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [ChIP-seq] |
| GSE234295 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF |
|
| Relations |
| BioSample |
SAMN35646838 |
| SRA |
SRX20602153 |
