|
Status |
Public on Oct 01, 2020 |
Title |
Control_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: control
|
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 |
SAMN10267779 |
SRA |
SRX4913527 |