|
| Status |
Public on Mar 01, 2024 |
| Title |
H1 ESCs, H3K27ac, XMD.2 |
| Sample type |
SRA |
| |
|
| Source name |
H1
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K27ac (abcam#ab4729)
cell line: H1
cell type: Human embryonic stem cells
genotype: WT
treatment: XMD892 1 uM treatment for 24h
|
| Treatment protocol |
XMD892 1uM was treated with E8 medium for 12/24/48hr in H1 ESCs.
|
| Growth protocol |
H1 ESCs was maintained in E8 medium supplemented with antibiotics with 5% CO2 at 37C. E8 medium contained DMEM/F12, sodium selenite, ascorbic acid trisodium, transferrin, insulin, FGF2 and TGFβ.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
H1 ESCs was processed cross-linking reaction by 1 % PFA and 125 mM Glycine. Cell lysates were sonicated with Diagenode BioRuptor Sonicator.
ChIP-seq library building was processed as published (Xu, Ye et al. 2020). The DNA library was generated by Tn5. The DNA library was sequenced using Illumina Novaseq 6000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
All raw data was subjected to Fastp
Differential enriched peaks (FDR) Reads were identified through MCAS2
ChIPseeker v1.32.1 was used to identify the promoter and annotate the features of peaks
the alignment results were converted to bigwig format using a series of softwares, e.g., MACS2 bdgcmp, Bedtools slop v2.29.0 and UCSC toolkits (http://hgdownload.cse.ucsc.edu/admin/exe/) including bedClip V 332 and Bedgraphtobigwig V 323
The peaks and alignment results were visualized through IGV v2.6.3
Assembly: hg38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Chengcheng SONG |
| E-mail(s) |
chengchengsong2021@gmail.com
|
| Phone |
62167066
|
| Organization name |
university of macau
|
| Department |
fhs
|
| Street address |
universtiy of macau
|
| City |
macau |
| ZIP/Postal code |
999078 |
| Country |
Macau |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE234055 |
ERK5 sustains autocrine mitogenic balance for cell fate specification in human pluripotent stem cells [ChIP-seq] |
| GSE234058 |
ERK5 sustains autocrine mitogenic balance for cell fate specification in human pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN35572971 |
| SRA |
SRX20579941 |
