|
| Status |
Public on Aug 27, 2022 |
| Title |
Naive KLF4 KLF5 DKO rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Naive H1 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
culture condition: FINE
genotype: KLF4 -/- KLF5 -/-
passage number: P12
|
| Treatment protocol |
KLF4 and/or KLF5 were knocked out by CRISPR-CAS9, and knockout lines or wild type lines were adapated in FINE naïve culture condition.
|
| Growth protocol |
Primed ESCs were grown in mTeSR till reaching 60-70% confluency, and naïve ESCs were grown in FINE culture condition after research 50% confluency
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent and purified.
library was prepared according to illumina RNAseq non-stranded Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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). Annotation for genes were from Ensembl (Yates et al., 2020) by using GRCh38.97. Annotation for transposable elements (TE) were based on repeatmasker (http://repeatmasker.org/) by using GRCh38.
Counts for both gene and transposable elements were calculated (parameters for gene “-p -B -P -C”, parameters for TE “-p -B -P -C -M”) by FeatureCounts v2.0.0 (Liao et al., 2014).
Differentially expressed genes (DEG) and transposable elements (DETE) were generated by R package DESeq2 v1.26.0 (Love et al., 2014) with 2 fold change and 0.05 FDR.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; count file 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) |
| GSE169675 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency [RNA-seq] |
| GSE169678 |
Krüppel-like factor 5 rewires NANOG regulatory network to activate human morulablastocyst specific LTR7Y and promote naïve pluripotency |
|
| Relations |
| BioSample |
SAMN18497811 |
| SRA |
SRX10448069 |
