|
| Status |
Public on Nov 06, 2019 |
| Title |
N3_IL10 |
| Sample type |
SRA |
| |
|
| Source name |
N3
|
| Organism |
Mus musculus |
| Characteristics |
mouse id: N3
cell type: Treg cells
tissue: Spleen
timepoint: Day 14 p.i.
infected with: Leishmania donovani
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were homogenised in QIAshredder (QIAGEN) columns, followed by RNA extraction using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions. Total RNA was treated with the RNase-free DNase Set (QIAGEN).
mRNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a)
Sequence reads were aligned to the GRCm38.70.dna.primary assembly with the gene, transcript, and exon features of GRCm38.70 gene model
Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCm38.70.dna.primary
Supplementary_files_format_and_content: tab-seperated values file includes unfiltered, normalised counts per million (cpm)
|
| |
|
| Submission date |
Nov 05, 2019 |
| Last update date |
Nov 07, 2019 |
| Contact name |
Susanna Ng |
| E-mail(s) |
susanna.ng@qimrberghofer.edu.au
|
| Organization name |
QIMR Berghofer Medical Research Institute
|
| Department |
Immunology
|
| Lab |
Immunology and Infection Lab
|
| Street address |
300 Herston Road
|
| City |
Herston |
| State/province |
QLD |
| ZIP/Postal code |
4006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE139933 |
The transcriptomic differences between Th1, Tr1, Treg, and Tneg cells in Leishmania donovani-infected mice |
|
| Relations |
| BioSample |
SAMN13198156 |
| SRA |
SRX7100539 |
