|
| Status |
Public on Jan 01, 2018 |
| Title |
HepG2_siHOTAIR-3 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2_siHOTAIR
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
cell type: Hepatocellular carcinoma (HCC)
transfected with: siRNA targeting HOTAIR (siHOTAIR)
|
| Treatment protocol |
For siRNA-mediated gene knockdown, cells were transfected with siRNA targeting HOTAIR (siHOTAIR) or negtive control siRNA(siNC)
|
| Growth protocol |
Cells were cultured and maintained in Dulbecco’s modified Eagle’s high glucose medium (Gibco, Gaithersburg, MD) supplemented with 10% fetal bovine serum (Gibco), 50 U/ml penicillin and 50 mg/ml streptomycin at 37 °C in a humidified incubator in the presence of 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with Trizol reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer’s instructions. rRNA was subsequently eliminated with RiboMinusTM Transcriptome Isolation Kits for human (Thermo).
Sequencing libraries were generated using the a TruSeq Stranded total RNA sample preparation kit (Illumina, San Diego, CA) following the guidelines of the manufacturers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
HTSeq (version 0.6.1) (Anders et al., 2015) was utilized to calculate the number of aligned reads per gene. DEGs between two groups were identified using DEseq2
Clean reads were mapped to the human reference genome (hg19)
Genome_build: hg19
Supplementary_files_format_and_content:
siHOTAIR-vs-siNC.diff.txt: unfiltered data generated by DESeq
siHOTAIR-vs-siNC.DESeq.diff.txt: filtered "siHOTAIR-vs-siNC.diff.txt" data, according to q value and log2fold
siHOTAIR-vs-siNC.DESeq.diffFilter.txt: filtered "siHOTAIR-vs-siNC.DESeq.diff.txt" which only retain the information of differentially expressed genes.
|
| |
|
| Submission date |
Apr 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiong Qian |
| E-mail(s) |
[email protected]
|
| Phone |
02768780730
|
| Organization name |
Institute of Hydrobiology, the Chinese Academy of Sciences
|
| Street address |
Donghu South Road 7, Wuhan 430072, People’s Republic of China
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE98091 |
Transcriptomic analysis of the HOTAIR-regulated genes |
|
| Relations |
| BioSample |
SAMN06820824 |
| SRA |
SRX2754594 |
