|
Status |
Public on Jul 31, 2016 |
Title |
CXCR5+P14 #3 |
Sample type |
SRA |
|
|
Source name |
splenic CD8+ T cells
|
Organism |
Mus musculus |
Characteristics |
infection: Infected cxcr5 expression: CXCR5+ activation: Activated CD44+
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Spleens were collected from infected mice to prepare single cell suspension. Target cells of interest were then sorted using flow cytometry and RNA was extracted using RNAeasy Kit from Qiagen. PolyA RNA seq libraries prepared using Ilumina Stranded Sample prep, Protocol 15031047 RevD Sept 2012. c-bot clustering using 12pM of library pool. Illumina Protocol 15006165 Rev K Oct 2012.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
|
|
Description |
X5plus-3
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed with Trimmomatic-0.32 using a leading and trailling quality cutoff of 24. Trim_galore using a stringency of 3 to trim illumina adaptors. The reads were mapped to the mm10 reference genome using STAR. Reads were assigned to transcripts using HTSeq version 0.6.0 using the default setting. Genome_build: Mus Musculus.GRCm38.75. Supplementary_files_format_and_content: dyu_counts.txt
|
|
|
Submission date |
Dec 22, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Yew Ann Leong |
E-mail(s) |
yew.leong@monash.edu
|
Phone |
03 9902 4675
|
Organization name |
Monash University
|
Department |
BIochemistry
|
Lab |
Immunomodulation Laboratory
|
Street address |
Wellington Road
|
City |
Clayton |
State/province |
Victoria |
ZIP/Postal code |
3800 |
Country |
Australia |
|
|
Platform ID |
GPL18480 |
Series (1) |
GSE76279 |
CXCR5+ Follicular Cytotoxic T cells Control Viral Infection in B Cell follicles |
|
Relations |
BioSample |
SAMN04362875 |
SRA |
SRX1497700 |