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Sample GSM4743792 Query DataSets for GSM4743792
Status Public on Aug 25, 2020
Title PLZFpos_adipose1
Sample type SRA
 
Source name γδ T cells
Organism Mus musculus
Characteristics strain: C57Bl/6
gender: Male
tissue: Epididymal adipose
age: 16-22 weeks
cell type: PLZF+ {gamma}{delta} T cell subsets
Treatment protocol N/A
Growth protocol Male mice were fed ad libitum and sacrificed between 16-22 weeks of age.
Extracted molecule total RNA
Extraction protocol PLZF+ and PLZF- γδ T cells were sorted from the spleen, inguinal lymph nodes, lungs and adipose tissue of PLZF-GFP mice using a FACSAria Fusion into 5µl of TCL buffer into a 96 well plate.
RNA libraries were prepared for sequencing using Illumina SMARTseq2 protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description PLZFposAT1
Data processing Reads were mapped to the mouse genome (mm10) using HISAT (0.1.6-beta release).
Bam files were sorted and indexed by SAMtools (1.2 release).
Merged transcriptome (constructed from all samples that went through sequencing, only the samples described in the paper are deposited here) was used as a reference annotation for quantification, normalization and differential expression analysis.
Quantification and normalization were performed using CuffLinks (1.2 release), according to the Tuxedo pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet containing TMM-normalized gene expression values for each sample.
 
Submission date Aug 24, 2020
Last update date Aug 25, 2020
Contact name Lydia Lynch
Organization name Trinity College Dublin
Street address Trinity Biomedical Sciences Institute 152-160 Pearse St
City Dublin
ZIP/Postal code Dublin 2
Country Ireland
 
Platform ID GPL19057
Series (1)
GSE156782 Distinct metabolic programmes established in the thymus control the effector functions of γδ T cell subsets in tumour microenvironments
Relations
Reanalysis of GSM2780506
BioSample SAMN15894849
SRA SRX8999222

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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