|
| Status |
Public on Aug 11, 2023 |
| Title |
20764X15 Tet2KO_Th1_Secondary_Day7_biol_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6/J
Sex: female
tissue: Spleen
cell type: SMARTA CD4 T Cells
cell subset: Th1
genotype: Tet2 Knockout
infection: LCMV Armstrong
time: day 7 recall response
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was harvested from FACS sorted cells using the Quick-DNA MicroPrep Kit (Zymo Research)
10-200ng were fragmented by sonication (Covaris).Unmethylated cytosines were converted to uracils and sequencing libraries were created using the NEBNext Enzymatic Methyl Seq kit (New England Biolabs) according the manufacturer’s instructions. DNA libraries were sequenced using an Illumina NovaSeq 6000 system following the manufacturer’s protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing data quality was assessed using FastQC v0.11.4. Adapters were trimmed from the sequencing reads using Trim Galore!v0.4.4. Alignment to the mm10 reference genome was performed using Bismark v0.19.0. Deduplication was performed with deduplicate_bismark. Library quality was considered sufficient if greater than 50% of reads uniquely aligned to the genome. Bisulfite conversion efficiency was assessed by evaluating the percent of methylation observed in the CHH genome context and considered sufficient when this value was less than 3%. Library genome coverage was considered sufficient if 80% of the genome had a depth of at least 10 reads. CpG positions in the reference genome were quantified using the Bismark Methylation Extractor v0.19.0. This analysis pipeline was developed and executed in the Seven Bridges cloud platform, and included use of the Bismark Analysis public workflow. Differentially methylated regions (DMR) were detected using Bsmooth, Bsmooth.tst and dmrFinder in the bsseq R package
Assembly: mm10
Supplementary files format and content: Tab-delimited Bismark coverage file
Library strategy: Whole Genome Enzymatic Methyl-seq
|
| |
|
| Submission date |
Jul 31, 2023 |
| Last update date |
Aug 11, 2023 |
| Contact name |
Jeffrey Scott Hale |
| E-mail(s) |
[email protected]
|
| Phone |
801-587-1885
|
| Organization name |
University of Utah
|
| Department |
Pathology
|
| Lab |
Hale Lab
|
| Street address |
15 North Medical Drive
|
| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE239724 |
Tet2 deletion in CD4+ T cells disrupts Th1 lineage commitment in memory cells and enhances T follicular helper cell recall responses |
|
| Relations |
| BioSample |
SAMN36775313 |
| SRA |
SRX21201286 |
