|
| Status |
Public on Dec 31, 2022 |
| Title |
H9_WT |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9-WT
cell type: embryonic stem cells
|
| Treatment protocol |
iCas9 or idCas9 hESC lines were generated by transfecting with PB-TRE-CAS9-PGK-puro-T2A-rtTA (50 ng) or PB-TRE-dCAS9-PGK-puro-T2A-rtTA plasmids (50 ng) plus transposase mPB.Cas9 (dCas9) was inducible by doxycycline (Dox) in these cells.
|
| Growth protocol |
hESCs were cultured in matrigel-coated plates in the Essential 8TM hESC medium (Thermo, catalog. no. A1517001). The medium was changed daily. hESCs were treated with 0.48 mM EDTA for dissociation and then passaged onto new Matrigel -coated plates every 4–5 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from hESCs using the Trizol kit (Thermo Fisher Scientific, catalog. no. 15596018) following the manufacturer’s instructions. PolyA(+) RNA was isolated for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequencing quality of all high-throughput sequencing data were first comprehensively examined by FastQC. whose results were parsed using MultiQC. Next, adapter sequences and bases with sequencing quality < 20 were trimmed from raw data by TrimGalore.
Trimmed read pairs were aligned to genome with STAR.
We computed the number of mapping reads unambiguously attributed to each gene and repeat locus using the featureCounts package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Nov 17, 2020 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Denghui Chen |
| E-mail(s) |
chendh39@mail.sysu.edu.cn
|
| Organization name |
Sun Yat-sen University
|
| Department |
Zhongshan School of Medicine
|
| Street address |
No. 74 Zhongshan 2nd Road
|
| City |
Guangzhou City |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE161634 |
Cas9 interactions with host RNAs and transposable elements impair neurodevelopment (RNA-seq) |
| GSE161635 |
Cas9 interactions with host RNAs and transposable elements impair neurodevelopment |
|
| Relations |
| BioSample |
SAMN16817760 |
| SRA |
SRX9521159 |
