|
| Status |
Public on Aug 27, 2022 |
| Title |
Naive H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
Naive H1 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
culture condition: FINE
genotye: wild type
passage number: P15-20
antibody: H3K27ac
|
| Treatment protocol |
Naïve ESCs were fixed with 1% formaldehyde and quenched with glycine
|
| Growth protocol |
Human naïve ESCs were grown in FINE culture condition after research 50% confluency
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell pellets were lyzed and chromatin was pulled down by the respective antibodies
library was prepared according to illumina DNA sequencing Library Prep Kit
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
For sequence trimming, first 10bp and last 90bp were discarded by cutadapt v1.18 (Martin, 2011), based on quality control tool fastqc v0.11.8 (Andrews, 2010).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38. The reads was allowed to map to maximum of 1,000 loci and the best hit was kept (--outFilterMultimapNmax 1000 –outSAMmultNmax 1). Mapping reads over splice junction was not allowed by building STAR index without general feature format file and disallowing intron length (--alignIntronMax 1).
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.2.1 (Ramírez et al., 2014) was used to generate bigwig tracks.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with 4 fold change.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample
|
| |
|
| Submission date |
Mar 25, 2021 |
| Last update date |
Aug 27, 2022 |
| Contact name |
Xinyu Xiang |
| E-mail(s) |
[email protected]
|
| Phone |
+86 18106548581
|
| Organization name |
Zhejiang University
|
| Department |
Zhejiang University-University of Edinburgh Institute
|
| Street address |
East Haizhou Road
|
| City |
Haining |
| State/province |
- |
| ZIP/Postal code |
314400 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE169673 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [ChIP-seq] |
| GSE169678 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency |
|
| Relations |
| BioSample |
SAMN18497776 |
| SRA |
SRX10448025 |
