|
| Status |
Public on Jan 01, 2021 |
| Title |
Kap1 for over expression of ESC, Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
ESC
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESC
strain: 129Sv
genotype: Dcaf11 Over expression
chip antibody: Kap1 (Abcam no. ab22553)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and Kap1-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Normalized tag counts
|
| Data processing |
ChIP-seq reads were first removed adapters and low-quality base calls by trim_galore (version 0.4.2) using the default parameters.
Chip-seq reads were aligned to the mouse genome (mm9) using Bowtie2 v.2.3.5 with the parameters –no-mixed --no-discordant.
ChIP-seq peaks were called with MACS2 with the parameters –nomodel --keep-dup all --SPMR over input files
Genome_build: mm9
Supplementary_files_format_and_content: Signal track for each sample were generated using the “bamCoverage” function of deeptools and were normalized by calculating the reads per kilobase of transcript per million mapped reads (RPKM)
|
| |
|
| Submission date |
Nov 27, 2020 |
| Last update date |
Jan 03, 2021 |
| Contact name |
Yixin Huang |
| E-mail(s) |
1710944@tongji.edu.cn
|
| Organization name |
Tongji University
|
| Street address |
Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE132746 |
Dcaf11 facilitates telomere elongation in early embryos and embryonic stem cells (ESCs) through activating the Zscan4-mediated alternative lengthening telomere (ALT) mechanism |
| GSE162232 |
Kap1 ChIP-seq Analysis of Wild Type(WT) and Dcaf11 overexpresion(OE) ESCs |
|
| Relations |
| BioSample |
SAMN16935282 |
| SRA |
SRX9596424 |
