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Sample GSM8289074 Query DataSets for GSM8289074
Status Public on Oct 23, 2024
Title Sample 99
Sample type SRA
 
Source name Liver
Organism Homo sapiens
Characteristics tissue: Liver
Sex: Male
case/control: IMID-NAFLD
disease: NAFLD & Hidradenitis
fibrosis degree: F1
obesity: yes
t2d/ir: No
hypertension: No
fasting glycemia: 125
hba1c: 5.6
total cholesterol: 158
hdl-cholesterol: 44
ldl-cholesterol: 89
tryglicerides: 123
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 AR7271
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 SAMN41521511
SRA SRX24684300

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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