 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 20, 2021 |
| Title |
6T_cas9_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
tissue: Human embryonic kidney
treatment: PX330-GFP-cas9-6T-sgRNA
|
| Treatment protocol |
HEK293T cells were seeded into 6-well plates one day prior to transfection, and transfected at 70-80% confluency using Polyethylenimine (PEI, Polysciences, Inc.USA) followed by the manufacturer’s protocol. For each well of a 6-well plate, 2 μg DNA and 6 μl PEI were used.
|
| Growth protocol |
HEK293T cell line was grown in Dulbecco’s modified Eagle’s Medium (DMEM, Thermo Fisher Scientific ,Waltham, USA) with 10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin at 37 °C in a 5% CO2 atmosphere.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
HEK293T cells were washed in ice-cold 1× PBS solution, and total RNA was isolated using Trizol according to the manufacturer’s instructions (Life Technologies, MA, USA). DNA was removed using the Ambion TURBO DNA-free Kit (Life Technologies, MA, USA). cDNA libraries were obtained using the VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina ® (Vazyme Biotech Co., Ltd., Jiangsu, China) from 1μg RNA following the manufacturer’s recommendations.
RNA libraries were prepared according to instructions of VAHTS mRNA-seq library prep kitfor illumina (Vazyme, NR601).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing reads were mapped to hg8 with STAR by default parameter. The read counts for each genes were calculated by HTSeq-count. The count files were used as input to DESeq for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: DESeq was used for calling differential expression. Text files include normalized read counts, foldChange, pvalue ('cas9' represents the 'A' group, 'nocas9' represents the 'B' group).
|
| |
|
| Submission date |
Mar 20, 2018 |
| Last update date |
Mar 20, 2021 |
| Contact name |
Zaijun Ma |
| E-mail(s) |
[email protected]
|
| Organization name |
Chinese Academy Science
|
| Street address |
Qiuyue Road 26
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE112076 |
Multi-omic analyses reveal minimal impact of the CRISPR-Cas9 nuclease on the host |
|
| Relations |
| BioSample |
SAMN08742817 |
| SRA |
SRX3823751 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
