 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 12, 2019 |
| Title |
STAT1-KO_UN |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 cell lines
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: hepatocellular carcinoma
genotype: STAT1 knockout
treatment: untreated
|
| Treatment protocol |
cells were with/without 1000 U/ml IFNα for 6 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
HepG2 cells, SETD2-KO, STAT1-KO, and K525A-Re cells (with or without IFNa treatment) were removed, flash frozen on dry ice, and RNAs were harvested using Trizol reagent. 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 |
BGISEQ-500 |
| |
|
| Data processing |
BGISEQ-500 basecalling software
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped clean reads to whole hg38 gene using Bowtie2 and to hg38 genome using HISAT.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated as described in Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
May 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
kun chen |
| E-mail(s) |
kunc109727@163.com
|
| Phone |
+8615900809470
|
| Organization name |
Zhejiang University
|
| Street address |
No.800 Xiangyin Road, Yangpu District
|
| City |
shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE98372 |
Next Generation Sequencing Facilitates Quantitative Analysis of IFNα Stimulated Transcriptomes in HepG2, SETD2-KO, STAT1-KO and STAT1-K525ARe HepG2 cells |
|
| Relations |
| BioSample |
SAMN06854105 |
| SRA |
SRX2771252 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2592894_STAT1-KO_UN_FPKM.txt.gz |
98.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
