|
| Status |
Public on Jan 09, 2022 |
| Title |
TBRT2203_34 |
| Sample type |
SRA |
| |
|
| Source name |
Liver biopsy tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver
timing of biopsy: pre-treatment
fibrosis improvement: NA: pre-treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from fixed tissue specimens using High Pure RNA Paraffin Kit (Roche) and quantified by qubit (Thermo Fisher). Only RNA samples with DV200 > 30% by Agilent 2100 bioanalyzer were used.
RNA-Seq libraries were prepared by using TruSeq RNA Access kit following manufacturer's protocol.
Targeting genome-wide coding regions by capture probes. Single-end read of 75bp was performed by NextSeq genome sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
135-005_drugA_Baseline
|
| Data processing |
Raw sequencing reads were 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 raw read count for each gene
|
| |
|
| Submission date |
May 24, 2021 |
| Last update date |
Apr 08, 2022 |
| Contact name |
Yujin Hoshida |
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE85550 |
Molecular signature predictive of long-term liver fibrosis progression to inform anti-fibrotic drug development |
| GSE175448 |
Transcriptome profiles of liver biopsy tissues before and after cenicriviroc treatment in patients with non-alcoholic steatohepatitis |
|
| Relations |
| BioSample |
SAMN19317970 |
| SRA |
SRX10973804 |
