|
| Status |
Public on Oct 23, 2024 |
| Title |
Sample 103 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
Sex: Male
case/control: IMID-NAFLD
disease: NAFLD & IBD
fibrosis degree: F1
obesity: no
t2d/ir: No
hypertension: yes
fasting glycemia: 77
hba1c: 5
total cholesterol: 171
hdl-cholesterol: 72
ldl-cholesterol: 89
tryglicerides: 51
|
| Treatment protocol |
Total RNA was obtained from freshly frozen biopsies
|
| Growth protocol |
Liver biopsies were obtained percutaneously with a Tru-Cut biopsy needle following a standard procedure in patients with suspected significant liver fibrosis according to liver stiffness measurement (LSM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly frozen biopsies were disrupted using Kimble® Pellet Pestle® Cordless Motor (DWK Life Sciences, Cat. No.: 749540-0000). RNA extraction was performed using the PureLink™ RNA Mini Kit (Invitrogen, Cat. No.: 12183018A) adding an extrapurification process with the PureLink™ DNase Set (Invitrogen, Cat. No.: 12185010).
RNA-seq reads were mapped against the human reference genome (GRCh38) using STAR (version 2.5.3a) with ENCODE parameters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AR7275
|
| Data processing |
Genes were quantified using RSEM (version 1.3.0) with default parameters.
The human gene annotation file was downloaded from gencode release 36 (https://www.gencodegenes.org/).
Mapping and quantification quality checking were performed with GEMTools (https://gemtools.github.io/) and custom python scripts.
A multidimensional scaling plot was performed to inspect sample similarities using the ‘voom’ transformed counts and the top 500 most variable genes.
Assembly: Human reference genome (GRCh38)
Supplementary files format and content: EGN_RNAseq_Normalized_data: Excel file incuding gene normalized expression for each sample.
Supplementary files format and content: EGN_RNAseq_Processed_data: Differential gene expression (IMID-NAFLD vs. Classic-NAFLD) adjusted for BMI, sex, and fibrosis severity.
|
| |
|
| Submission date |
May 24, 2024 |
| Last update date |
Oct 23, 2024 |
| Contact name |
Enrique García Nieto |
| E-mail(s) |
[email protected]
|
| Organization name |
Instituto de Investigación Marqués de Valdecilla
|
| Street address |
C. Cardenal Herrera Oria, s/n
|
| City |
Santander |
| State/province |
Cantabria |
| ZIP/Postal code |
39011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE268273 |
Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases |
|
| Relations |
| BioSample |
SAMN41521507 |
| SRA |
SRX24684249 |
