|
| Status |
Public on Apr 04, 2019 |
| Title |
HepG2_HCF1si_4 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2_HCF-1 siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2
treatment: HCF-1 siRNA
|
| Treatment protocol |
For siRNA transfection, HepG2 cells were reverse transfected using siPORT NeoFX (Invitrogen). The transfection procedure was repeated two days later, and RNA extraction was performed two days after the second transfection.
|
| Growth protocol |
For RNA-seq, eight biological replicates were used for each condition. HepG2 cells were maintained in EMEM supplemented with 10% final concentration of fetal bovine serum (FBS) and 1% penicillin-streptomycin in a humidified incubator with 5% CO2 at 37˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA-seq libraries were constructed using TruSeq Stranded mRNA (Illumina) according to manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
20181106_HCF1si_4
|
| Data processing |
RNA samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (v0.9.1a; https://bcbio-nextgen.readthedocs.org/en/latest/).
Adapter sequences were trimmed from reads using Cutadapt (v1.4.2) (Martin, 2011).
Trimmed reads were aligned to the hg19 genome using STAR (v2.4.1d) (Dobin et al., 2013).
Read quantitation was performed with featureCounts (v1.4.4) (Liao et al., 2014).
Differential expression of genes was performed using DESeq2 (v1.16.1) (Love et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: CSV matrix file of normalized counts generated using DESeq2.
|
| |
|
| Submission date |
Jan 09, 2019 |
| Last update date |
Apr 04, 2019 |
| Contact name |
John G Flanagan |
| E-mail(s) |
[email protected]
|
| Phone |
6174320330
|
| Organization name |
Harvard Medical School
|
| Department |
Cell Biology
|
| Lab |
Flanagan
|
| Street address |
200 Longwood Ave, Building C2, Room 523
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE107336 |
Insulin receptor associates with promoters genome-wide and regulates gene expression |
| GSE124845 |
Insulin receptor associates with promoters genome-wide and regulates gene expression [RNA-seq 2] |
|
| Relations |
| BioSample |
SAMN10717645 |
| SRA |
SRX5232063 |
