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| Status |
Public on Oct 03, 2023 |
| Title |
GN178_Vg4_biol_rep_1 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon
cell type: Vg4+ gd T cells
treatment: non-inflamed; non-transformed
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| 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
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| Submission date |
Nov 21, 2022 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Adrian Hayday |
| Organization name |
King's College London
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| Department |
Immunobiology
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| Street address |
Great Maze Pond
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| City |
London |
| ZIP/Postal code |
SE1 9RT |
| Country |
United Kingdom |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE218446 |
Gene expression analysis of Vg4+ vs Vg5/8/9+ gd T cells isolated from human gut |
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| Relations |
| BioSample |
SAMN31815643 |
| SRA |
SRX18327669 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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