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Sample GSM6112226 Query DataSets for GSM6112226
Status Public on Apr 04, 2024
Title P51-NAFLD-D-SITTC9
Sample type SRA
 
Source name liver biopsy
Organism Homo sapiens
Characteristics tissue: liver
disease status: NAFLD
patient id: P51
liver lobe: Right
gender: M
saf score: S1A1F1
age: 57
Treatment protocol Biopsies were snap frozen in liquid nitrogen
Extracted molecule total RNA
Extraction protocol Tissue lysis by dounce homogenisation and nuclei isolation by flow cytometry using scatter properties and DAPI staining to label nuclei.
Single-nuclei RNA-seq libraries were prepared using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, Chromium Chip G Kit and Chromium Single Cell 3' Reagent Kits v3.1 User Guide (Manual Part CG000316 Rev A; 10X Genomics). For each sample 16k nuclei were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing nuclei cells. RNA from the barcoded nuclei for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-nuclei libraries were performed according to the manufacturer’s protocol with 19 PCR cycles in cDNA amplification step. cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer (ThermoFisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration pool was qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing. Pool was sequenced on Illumina NovaSeq6000 sequencer with following parameters: 28 bp, read 1; 10 bp, i5 index; 10bp, i7 index; 90 bp, read 2
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Quality control was peformed using fastQC ( v0.11.8) and multiQC (v 1.9)
Alignment, filtering and gene quantification was performed using 10x cellranger v5.0.0; the alignment was perfomed against the H Sapiens reference genome (GRCh38.p13)
Normalization of expression was levels was performed with SCTransform (Hafemeister and Satija, 2019)
Clustering was performed using SLM algorithm from the FindClusters function from Seurat (Satija, 2021)
Differential Expression was perfored using the Wilcoxon Rank Sum test from FindMarkers function from Seurat (Satija, 2021)
Assembly: GRCh38.p13
Supplementary files format and content: Raw and norrmalised count matrices, in csv format
 
Submission date May 06, 2022
Last update date Apr 04, 2024
Contact name Irina Mohorianu
E-mail(s) data-submissions@stemcells.cam.ac.uk
Organization name University of Cambridge
Department Wellcome-MRC Cambridge Stem Cell Institute
Street address Puddicombe Way
City Cambridge
ZIP/Postal code CB2 0AW
Country United Kingdom
 
Platform ID GPL24676
Series (1)
GSE202379 Single Nuclei RNA-Seq to map progression of non-alcoholic fatty liver disease (NAFLD) in patients II
Relations
BioSample SAMN28116278
SRA SRX15196915

Supplementary file Size Download File type/resource
GSM6112226_D-SITTC9-norm_counts.csv.gz 4.1 Mb (ftp)(http) CSV
GSM6112226_D-SITTC9-raw_counts.csv.gz 5.2 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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