|
| Status |
Public on Jul 19, 2021 |
| Title |
Huh751_D10_1 |
| Sample type |
SRA |
| |
|
| Source name |
Huh751_D10_1
|
| Organism |
Homo sapiens |
| Characteristics |
objective response: Huh751 DMSO differentiation Day 10 Replicate 1
cell line: Huh751
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from each sample was collected using TRIzol (Invitrogen) and quantified by nanodrop (Thermo Fisher). Only RNA samples with RNA integrity number (RIN) > 9 by Agilent 2100 bioanalyzer (Cat# G2939BA, Agilent Technologies) were used.
RNA-Seq libraries were prepared by using TruSeq kit (Cat# RS-122-2001, Illumina)
NextSeq genome sequencer (Cat# SY-415-1002, Illumina), 75nt, Single-End Read, 4 samples per lane
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
The Illumina TruSeq RNA kit was used for 75nt/single end reads, 4 samples were run per lane using the standard Truseq indices. Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: hg19
Supplementary_files_format_and_content: txt format; the read count for each gene
|
| |
|
| Submission date |
Mar 17, 2021 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Shijia Zhu |
| E-mail(s) |
shijia.zhu@utsouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
DALLAS |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE66843 |
A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention |
| GSE169084 |
A human liver cell-based system modeling a clinical prognostic liver signature combined with single-cell RNA-Seq for discovery of liver disease therapeutics |
|
| Relations |
| BioSample |
SAMN18334892 |
| SRA |
SRX10366604 |
