|
| Status |
Public on Jul 01, 2022 |
| Title |
HUnafld105 |
| Sample type |
SRA |
| |
|
| Source name |
HUnafld105
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
biopsy: 1st biopsy
age: 38
Sex: male
fibrosis stage: 2
nafld activity score: 3
pls-nafld-based risk prediction at 1st biopsy: low-risk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 10 micron-thick FFPE tissue using High Pure RNA Paraffin kit (Roche) according to manufacturer’s protocol.
Truseq RNA Exome kit (Illumina, CA) following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
NAFLD.HUn106.gct
NASH.HUn164.gct
|
| Data processing |
Raw cDNA reads are aligned to the reference genome (hg19) using the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the gene levels. The count data were normalized using “Relative Log Expression” normalization (RLE) implemented in the DESeq2 R package. Poor-quality transcriptome profiles were determined based on inter-sample correlation <0.7 and excluded from the subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: .gct file format (tab-delimited text) including normalized gene expression levels normalized within 106 1st biopsy tissues (NAFLD.HUn106.gct) and within the 58 high-risk patients with paired biopsy tissues (NAFLD.HUn164.gct).
|
| |
|
| Submission date |
Jan 05, 2022 |
| Last update date |
Jul 01, 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 |
GPL18573 |
| Series (2) |
| GSE193066 |
Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 1). |
| GSE193084 |
Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease |
|
| Relations |
| BioSample |
SAMN24648757 |
| SRA |
SRX13614063 |
