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Sample GSM2780509 Query DataSets for GSM2780509
Status Public on May 10, 2018
Title PLZFneg_adipose2
Sample type SRA
Source name γδ T cells
Organism Mus musculus
Characteristics strain: C57Bl/6
gender: male
tissue: Epididymal adipose
age: 16-22 weeks
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 adipose tissue of PLZFGFP 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
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 samplesthat went through sequencing, only the samples described in the paper are deposited here) was used as a reference annotation for quantification, normlalization and differential expression analysis.
Quantification and normalization were performed using CuffLinks (1.2 release), according to the Tuxedo pipeline.
Differentially expressed genes between PLZF+ and PLZF- γδ T cell subsets were identified using CuffDiff (false-discovery rate and adjusted p-value < 0.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each analyzed γδ T cell comparison
Submission date Sep 12, 2017
Last update date Aug 24, 2020
Contact name Tal Shay
Phone +972-8-6461277
Organization name Ben-Gurion University
Department Life scuences
Lab Tal Shay
Street address Ben Gurion
City Be'er Sheva
ZIP/Postal code 8410501
Country Israel
Platform ID GPL19057
Series (1)
GSE103742 γδ T cells producing IL-17A regulate adipose Treg homeostasis and thermogenesis
Reanalyzed by GSM4743796
BioSample SAMN07634101
SRA SRX3179284

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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