|
| Status |
Public on Jun 15, 2022 |
| Title |
KO Tfh #3 (18010X16) |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tet2 KO
strain: C57BL/6
cell type: Mouse SMARTA CD4 T Cells
cell subset: Tfh
agent: LCMV Armstrong
time point: 7 days post infection
Sex: Female
id for sequencing: 18010X16
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was harvested from FACS sorted cells using Dneasy Blood and Tissue Kit (Qiagen). DNA inputs of 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 |
Library strategy: Enzymatic Methyl-seq
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
Genome_build: mm10
Supplementary_files_format_and_content: BED file from Bismark Methylation Extractor
|
| |
|
| Submission date |
Aug 27, 2021 |
| Last update date |
Jun 15, 2022 |
| Contact name |
Jeffrey Scott Hale |
| E-mail(s) |
scott.hale@path.utah.edu
|
| 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 (2) |
| GSE182940 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation (Methyl-Seq) |
| GSE183317 |
Tet2-mediated epigenetic programing of T follicular helper cell differentiation |
|
| Relations |
| BioSample |
SAMN21024286 |
| SRA |
SRX11952359 |
