|
| Status |
Public on Aug 27, 2022 |
| Title |
Naïve KLF4KLF5DKO NANOG |
| Sample type |
SRA |
| |
|
| Source name |
Naïve H1 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
culture condition: FINE
genotype: KLF4 -/- KLF5 -/-
passage number: P15-P20
|
| Treatment protocol |
CRISPR-Cas9-mediated knockout of KLF4KLF5 in naïve hESCs
|
| 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: CUT&Tag
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For sequence trimming, Tn5 adapter (AGATGTGTATAAGAGACAG) was trimmed by cutadapt v1.18 (Martin, 2011).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1). By creating STAR index without general feature format file and not allowing intron length (--alignIntronMax 1), the splice junction was neglected.
PCR duplicates were removed by Samtools v1.2 (Li et al., 2009) rmdup function.
Deeptools v3.4.3 (Ramírez et al., 2014) was used to generate bigwig tracks by normalizing to RPKM using binsize of 10bp.
Peaks were identified by callpeaks function of MACS2 v2.2.7.1 (Zhang et al., 2008) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format; peak tracks for each sample
|
| |
|
| Submission date |
Dec 14, 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) |
| GSE169678 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency |
| GSE190882 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [CUT&Tag] |
|
| Relations |
| BioSample |
SAMN24023371 |
| SRA |
SRX13437670 |
