|
| Status |
Public on May 31, 2019 |
| Title |
PP_CD4_3 |
| Sample type |
SRA |
| |
|
| Source name |
Peyer's Patch CD4 T-cells
|
| Organism |
Mus musculus |
| Characteristics |
tag: CD4 T-cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peyer’s patch cells and spleen cells were prepared from 3 littermate Va14 female mice. Cell preparations were stained with CD1d-PBS57 tetramer and antibodies to CD4, CD45, and CD3. iNKT cells were sorted by FACS from both tissues and CD4+CD1dtet- cells were sorted from Peyer’s patches into collection tubes containing RNA isolation buffer (Qiagen RNA mini plus).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Peyer's Patch CD4 T-cells
|
| Data processing |
Reads were mapped to the mm10 transcriptome using Salmon (0.8.2) with default flags.
Transcript-level quantifications were transformed to gene-level quantifications in R using the tximport (1.10.1) package.
Genes that had less than 10 reads in total across all samples were filtered out.
DESeq2 (1.22.2) was used to perform differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: CSV of log2 normalized counts for each gene (one file per sample)
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
May 31, 2019 |
| Contact name |
Stephanie Dougan |
| E-mail(s) |
[email protected]
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Cancer Immunology & Virology
|
| Street address |
1 Jimmy Fund Way
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE129366 |
Transnuclear mice reveal a population of Peyer’s patch iNKT cells that regulate B cell class switching to IgG1 |
|
| Relations |
| BioSample |
SAMN11347978 |
| SRA |
SRX5644997 |
