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Sample GSM4417229 Query DataSets for GSM4417229
Status Public on Apr 22, 2020
Title Donor 4 CD26+ CD94lo +IL2 +IL23 (D4 26 IL2 IL23)
Sample type SRA
 
Source name Human PBMC
Organism Homo sapiens
Characteristics tissue: PBMC
cell type: CD3+ Vd2+ CD26+ CD94lo +IL2 +IL23
Extracted molecule total RNA
Extraction protocol RNA was isolated from sorted cells using a Zymo Direct-zol RNA MicroPrep Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Sample 19
Degust_Voom_Limma - IL23 expansion.csv, Raw counts - IL23 expansion.txt
Data processing RNAseq analysis was performed using the web-based Galaxy platform maintained by Galaxy Australia.
Reads were mapped to the Homo sapiens reference genome (hg38) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: hg38
Supplementary_files_format_and_content: CSV/tab-delimited text files include raw counts or CPM values
Supplementary_files_format_and_content: Degust_Voom_Limma - IL23 expansion.csv: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw counts - IL23 expansion.txt: Raw counts - Htseq
 
Submission date Mar 17, 2020
Last update date Apr 22, 2020
Contact name Hyon Xhi Tan
E-mail(s) hxtan@unimelb.edu.au
Organization name The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity
Department Department of Microbiology and Immunology
Street address 792 Elizabeth St
City Melbourne
State/province Victoria
ZIP/Postal code 3010
Country Australia
 
Platform ID GPL24676
Series (1)
GSE122409 High CD26 and low CD94 expression identifies an IL-23 responsive V(delta)2+ T cell subset with a MAIT cell-like transcriptional profile
Relations
BioSample SAMN14390723
SRA SRX7925016

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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