|
| Status |
Public on Dec 18, 2018 |
| Title |
S433WT3Spl |
| Sample type |
SRA |
| |
|
| Source name |
WT_Spleen Rep3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: Treg
genotype: WT (Foxp3Cre-YFP)
|
| Growth protocol |
Treg cells were sorted as CD4+ TCRb+ YFP+ cells from gut or spleen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 1 or greater in at least two libraries. The Ig genes, pseudo genes, gene models, genes not on the primary assemblies of the chromosomes, genes not having official symbols and ribosomal RNA genes were also removed from the analysis.
Counts were converted to log2 counts per thousand bases per million fragments (log2 FPKM), quantile normalized and precision weighted with the ‘voom’ function of the limma package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 (adjusted globally) or less and had an expression change of two folds or greater.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.
|
| |
|
| Submission date |
Nov 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE106396 |
c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis |
|
| Relations |
| BioSample |
SAMN07962634 |
| SRA |
SRX3349443 |
