|
| Status |
Public on Oct 01, 2020 |
| Title |
ZFP90-KO _2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: human colorectal cancer cells
passage: 16-19
genotype/variation: ZFP90 KO
|
| Treatment protocol |
To create ZFP90-Knockout alleles in HCT116, sgRNA were designed to target exon 3 of ZFP90
|
| Growth protocol |
The human HCT116 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of HCT116 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file
|
| |
|
| Submission date |
Oct 22, 2018 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Haoyan Chen |
| Organization name |
Renji Hospital
|
| Street address |
145 Shandong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE121621 |
ZFP90 promotes colorectal carcinogenesis and stemness [RNA-seq] |
| GSE121624 |
ZFP90 promotes colorectal carcinogenesis and stemness |
|
| Relations |
| BioSample |
SAMN10267776 |
| SRA |
SRX4913530 |
