|
| Status |
Public on Mar 01, 2023 |
| Title |
human liver sample A2008279 |
| Sample type |
SRA |
| |
|
| Source name |
liver cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: liver cells
fibrotic stage: F3F4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from liver tissues or hepatocytes as previously described
Libraries were made with NEBNext Ultra RNA Library Prep Kit from Illumina. Sample qualities were assessed by Agilent RNA Bioanalyzer chip traces before pooled and sequenced with an Illumina HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequencing reads were trimmed using TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and aligned to the mm10 reference genome using STAR
Gene expression counts were generated using HTSeq and DEseq2 was used to perform differential expression analyses (absolute log2FC >= 1 and q <0.05)
Assembly: hg39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Sep 19, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Anna Mae Diehl |
| E-mail(s) |
annamae.diehl@duke.edu
|
| Organization name |
Duke University
|
| Street address |
905 S LaSalle St
|
| City |
Durham |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE213621 |
Hepatocyte Smoothened Activity Controls Susceptibility to Insulin Resistance and Nonalcoholic Fatty Liver Disease [RNA-Seq] |
| GSE213623 |
Hepatocyte Smoothened Activity Controls Susceptibility to Insulin Resistance and Nonalcoholic Fatty Liver Disease |
|
| Relations |
| BioSample |
SAMN30920955 |
| SRA |
SRX17623769 |
