|
| Status |
Public on Oct 20, 2021 |
| Title |
HD Tfh cell rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mesenteric lymph node
|
| Organism |
Mus musculus |
| Characteristics |
strain: FIR mice
tissue: mesenteric lymph node
post infection: 21 days
|
| Treatment protocol |
Mice were infected with either low dose/LD/30 or high dose/HD/200 parasitic eggs and culled 21 days after infection, and mesentric lymph nodes were extracted. Tfh cells (CD4+ CD44hi FOXP3- Ly6C- CD162- PD-1+ CXCR5+) at d21 pi and naive Th cells (CD4+ FOXP3- CD44low CD62Lhigh ) from uninfected mice were FACS-sorted and purified for RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from FACS-sorted cells was extracted using Rneasy Plus Micro Kit (QIAGEN) as per manufacturers’ standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Description |
1247_S5
|
| Data processing |
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al., 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GRCm38 was used
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts, text file, tab separated
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Aidil Zaini |
| E-mail(s) |
muhammad.binahmadzaini@Monash.edu
|
| Phone |
0452515127
|
| Organization name |
MONASH UNIVERSITY
|
| Department |
BIOCHEMISTRY AND MOLECULAR BIOLOGY
|
| Lab |
Zaph Lab
|
| Street address |
LEVEL 3, BUILDING 77, MONASH UNIVERSITY
|
| City |
CLAYTON |
| State/province |
VICTORIA |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30215 |
| Series (1) |
| GSE185992 |
Transcriptomic profile of Tfh cells during intestinal helminth infection |
|
| Relations |
| BioSample |
SAMN22328424 |
| SRA |
SRX12633251 |
