|
| Status |
Public on Nov 29, 2024 |
| Title |
RNA-seq_PRDM1beta-OE-Ctrl-2 |
| Sample type |
SRA |
| |
|
| Source name |
ESC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ESC
genotype: wild type
|
| Treatment protocol |
Reprogramming intermediate population was collected by magnetic-activated cell sorting (MACS) through Pluripotent Stem Cell MicroBeads (Miltenyi Biotec) according to the manufacturer’s instructions. Naïve hESCs(knockdown and overexpression cell lines) were harvested directly for RNA extraction.
|
| Growth protocol |
hiF-T cells were seeded on feeder cells, then cultured in hESM + Doxycycline (Dox, 1 ng/mL) for 6 days, followed by either culturing as before to generate primed iPSCs or switching to 5iLAF medium to generate naive iPSCs. Naïve hESCs were cultured in 5iLAF medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by RNAiso Plus (Takara) following the manufacturer’s instructions.
Bulk mRNA-seq libraries were prepared by KAPA mRNA HyperPrep Kit (Kapa Biosystems) following the manufacturer’s instructions. Libraries were submitted to paired-end sequencing on the NovaSeq 6000 platform (Illumina) according to the manufacturer’s instructions at Berry Genomics Corporation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC hg19) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal.
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20.
The retained reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4).
The expression level of each gene was quantified as FPKM (fragments per kilobase per million mapped reads).
Assembly: hg19
Supplementary files format and content: tab-delimited files include FPKM values for all genes.
|
| |
|
| Submission date |
Feb 15, 2024 |
| Last update date |
Nov 29, 2024 |
| Contact name |
Liping Wang |
| E-mail(s) |
wanglp13@gmail.com
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200082 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE255861 |
The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming [RNA-seq] |
| GSE255862 |
The divergent role of two PRDM1 isoforms during human naïve pluripotency reprogramming |
|
| Relations |
| BioSample |
SAMN39956171 |
| SRA |
SRX23637754 |
