|
| Status |
Public on Aug 27, 2022 |
| Title |
Naïve |
| Sample type |
SRA |
| |
|
| Source name |
Naive H1 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
culture condition: FINE
genotye: wild type
passage number: P16
|
| Treatment protocol |
Primed ESCs were transduced with virus controling empty pLVTH or pLVTH-KLF5 for four days before collcted for ATAC-seq
|
| Growth protocol |
Primed ESCs were seeded in mTeSR at 0.15 million cells per ml; naïve ESCs were seeded in FINE medium at 0.15 milliom per ml.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
hESC pellet was lyzed; nuclei were isolated and treated with Tn5
libraries were prepared according to MagicSeq 619 Tn5 DNA Library Prep Kit for Illumina
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adaptor sequence (CTGTCTCTTATACACATCT, AGATGTGTATAAGAGACAG) was removed and reads shorter than 30bp was discarded by cutadapt v1.18 (Martin, 2011), then quality control was performed by fastqc v0.11.8.
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 is not allowed by building STAR index without general feature format file and disallowing intron length (--alignIntronMax 1).
Only the open chromatin paired-reads with distance less than 100bp were kept.
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 |
GPL24676 |
| Series (2) |
| GSE169671 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [ATAC-seq] |
| GSE169678 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency |
|
| Relations |
| BioSample |
SAMN18497716 |
| SRA |
SRX10447603 |
