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Sample GSM6745456 Query DataSets for GSM6745456
Status Public on Oct 03, 2023
Title GN178_Vg589_biol_rep_1
Sample type SRA
 
Source name Colon
Organism Homo sapiens
Characteristics tissue: Colon
cell type: Vg5/8/9+ gd T cells
treatment: non-inflamed; non-transformed
Extracted molecule total RNA
Extraction protocol Colonic biopsies from 1 donors (GN178) were used fresh. Colonic biopsies from 3 of the donors (GN188; GN190 and GN192) were defrosted. Biopsies were dissociated with Miltenyi Biotec's tumour dissociation kit, stained with antibodies and sorted on BD FACS AriaII Cell Sorter.
NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 2000
 
Data processing The quality of the sequencing reads was examined using FastQC (v0.11.4) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Raw sequencing reads (100-nt, paired-end) were trimmed using Trimgalore (v0.4.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Traces of ribosomal DNA and mitochondrial DNA were removed using the Bowtie2 (v2.2.5) (Langmead et al., 2012).
Reads were aligned to the human reference genome GRCh38 using STAR (v2.5.3a) (Dobin et al., 2013) default setting. Duplicate reads were removed using theMarkDuplicates function of the Picard tools (v2.17.11) (http://broadinstitute.github.io/picard/).
Reads were annotated using the Partek E/M (Partek software) gene count. Differentially expressed genes (DEG) were identified using DESeq2 (v3.5)(Love et al., 2014). DEG with fold change >= 2 and FDR value <= 0.05 were used for pathway enrichment and gene ontology (GO) analysis. GO and pathway enrichment analysis was done using DAVID Bioinformatics Resources v6.8 (https://david.ncifcrf.gov/).
Assembly: GRCh38
Supplementary files format and content: Gene count and DEGs.xlsx, geme counts and DEG
 
Submission date Nov 21, 2022
Last update date Oct 03, 2023
Contact name Adrian Hayday
Organization name King's College London
Department Immunobiology
Street address Great Maze Pond
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
 
Platform ID GPL30173
Series (1)
GSE218446 Gene expression analysis of Vg4+ vs Vg5/8/9+ gd T cells isolated from human gut
Relations
BioSample SAMN31815642
SRA SRX18327670

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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