|
| Status |
Public on Nov 11, 2017 |
| Title |
Maf_flox_Foxp3yfpcre_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Maf_flox_Foxp3yfpcre
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6 (N5 backcross)
age: 13 weeks
genotype/variation: Mafflox/floxFoxP3-YFP-cre
cell type: CD4+FoxP3+CD62L- regulatory T cells from Peyer's patches
replicate: rep 2
|
| Growth protocol |
Animals were housed under specific pathogen-free conditions that excluded Helicobacter hepaticus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
~40,000 cPeyer's patch effector Tregs were isolated from mice and sort purified by FACS. RNA was isolated and purified from sorted cells using a hybrid protocol employing Trizol for collection and the Qiagen RNeasy Micro Kit per manufactuer's directions.
Libraries were constructed from RNA using the Clontech Ultra-Low Input mRNA Seq Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
MC-S61
|
| Data processing |
Aligned to mouse genome using Tophat 2.1.1 with parameters “--library-type fr-firststrand--no-novel-juncs -G”
Count reads in features from mm10 genome annotation using htseq-count 0.6.1 with options “-s yes -m union”
Read counts were filtered to remove lowly-expressed genes (with less than 1 count per million reads in 2 or more samples), normalized to library size, and statistical analysis performed using edgeR ver 3.14 with Fisher's Exact Test.
Genome_build: mm10
Supplementary_files_format_and_content: Matrices of raw and filtered / normalized read counts output from edgeR.
|
| |
|
| Submission date |
Aug 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria Ciofani |
| E-mail(s) |
maria.ciofani@duke.edu
|
| Organization name |
Duke University Medical Center
|
| Department |
Immunology
|
| Street address |
207 Research Drive, 128 Jones Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE102491 |
c-Maf-dependent transcripts in effector Tregs from Peyer's patches |
|
| Relations |
| BioSample |
SAMN07490267 |
| SRA |
SRX3085688 |
