|
| Status |
Public on Aug 27, 2022 |
| Title |
Primed KLF5OE rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Primed H1 human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Primed H1 human embryonic stem cells
culture condition: mTeSR
genotype: KLF5 OE
passage number: P45-P50
|
| Treatment protocol |
Primed ESCs were transfected with CRISPRa-LTR7Y or pLVTH-KLF5 plasmid for three days before collcted for RNA-seq
|
| 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 |
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For sequence trimming, first 10bp were discarded 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). TE annotation file GRCh38 from repeatmasker (http://repeatmasker.org/) and gene annotation file GRCh38.97 from Ensembl (Howe et al., 2021) was applied to all genomics analysis.
Quantification for both gene and TE were calculated by FeatureCounts v2.0.0 (Liao et al., 2014). For gene quantification, only unique mapped reads were included (-p -B -P -C), while for TE quantification, multiple mapped reads were also included (-p -B -P -C -M).
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by R package DESeq2 v1.26.0 (Love et al., 2014). Only features with mean RPKM greater than 1 in either control or treatment group were retained. Differentially expressed features were obtained from two-fold change and 0.05 FDR filtering criteria.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; count file 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) |
| 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 |
SAMN24023231 |
| SRA |
SRX13437658 |
