|
| 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 |
| E-mail(s) |
talshay@bgu.ac.il
|
| 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 |
|
| Relations |
| Reanalyzed by |
GSM4743796 |
| BioSample |
SAMN07634101 |
| SRA |
SRX3179284 |
