|
| Status |
Public on Oct 20, 2021 |
| Title |
High dose Tfh cell rep1 |
| 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 DNA extraction and purification.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from FACS-sorted cells was extracted using Illumina Nextera DNA Library Kit (FC121-1030) as per manufacturers’ standard protocol.
DNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
data was processed using the nfcore/atacseq pipeline version 1.2.1 (doi: 10.5281/zenodo.2634132), using the GRCm38 reference, calling narrow peaks.
Data visualization and exploration were performed on Degust (Powell, 2015) web tool.
Genome_build: GRCm38
Supplementary_files_format_and_content: wig files were generated using MACS2
Supplementary_files_format_and_content: Count tables for merged peaks across all replicates separately
Supplementary_files_format_and_content: peak annotation was performed using HOMER
|
| |
|
| Submission date |
Oct 18, 2021 |
| Last update date |
Oct 20, 2021 |
| Contact name |
Aidil Zaini |
| E-mail(s) |
[email protected]
|
| 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 |
GPL30172 |
| Series (1) |
| GSE186062 |
Chromatin accessibility profile of Tfh cells during intestinal helminth infection |
|
| Relations |
| BioSample |
SAMN22371133 |
| SRA |
SRX12669733 |
