|
| Status |
Public on Jun 24, 2024 |
| Title |
RNA_hESC_OE OTX2_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Human embryonic stem cells
genotype: OE OTX2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Nearly 100 EGFP-positive hESCs were collected as one biological replicate for RNA-seq library construction.
Cells were picked and transferred to lysis buffer, and poly(A)+ RNA was captured by oligo(dT) primers. First-strand cDNA was synthesized by reverse transcription and then amplified, purified and fragmented. Fragmented cDNA was processed to construct an RNA-seq library by using the NEBNext UltraII DNA Library Prep Kit (New England Biolabs, Cat# E7645L) according to the manufacturer’s protocol for sequencing on an Illumina NovaSeq 6000 sequencer with a 150 bp paired-end sequencing strategy.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA_hESC_OE_OTX2.count.csv
|
| Data processing |
Raw reads were retrieved from published datasets. Alignment was performed using STAR (v2.7.10b). The UCSC version hg19 and mm9 genome sequences were used for Homo sapiens and Mus musculus, respectively. Raw counts for gene expression were quantified using featureCounts (v2.0.4). Annotations were retrieved from UCSC genome browsers and TEtranscripts.
Assembly: hg19
Supplementary files format and content: csv, expression counts
|
| |
|
| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 24, 2024 |
| Contact name |
Fan Guo |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Department |
The State Key Laboratory of Stem Cell and Reproductive Biology
|
| Lab |
Group of Reproductive Epigenetics
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE224618 |
Divergent originations of parental DNA hydroxymethylation in human preimplantation embryos |
|
| Relations |
| BioSample |
SAMN41940667 |
| SRA |
SRX24993268 |
