|
| Status |
Public on Sep 06, 2022 |
| Title |
WT B cells, mock 4 days, bio rep 1 [A_WT_mock] |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
strain: C57BL/6J
cell type: B cells
genotype: Tet2/3 WT
treatment: Untreated
|
| Treatment protocol |
Cells were treated with vehicle or with 100 ug/mL L-ascorbic acid 2-phosphate at the beginning of culture
|
| Growth protocol |
Naïve B cells were co-cultured with irradiated 40LB stromal cells in the presence of recombinant mouse interleukin-4 (1ng/mL; Peprotech) in complete media (RPMI1640, 10% fetal bovine serum, 2mM GlutaMax, 1x non-essential amino acid, 1mM sodium pyruvate, 10mM HEPES, 50 ug/mL gentamicin, and 55 uM 2-mercaptoethanol). Cells were incubated at 37°C with 5% CO2 for 4 days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated with Qiagen Blood and Tissue kit.
Purified genomic DNA was bisulfite converted and used as template for PCR. PCR products were pooled and barcoded using the EXP-NBD104 kit from Oxford Nanopore, followed by ligation of adapters from the SQK-LSK-110 kit.
Bisulfite treatment followed by Nanopore sequencing with barcodes
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
MinION |
| |
|
| Data processing |
Guppy (v6.1.2)
Porechop (v0.2.4)
Nanofilt (v2.8.0)
nanoEM
minimap2 (v2.24)
samtools (v1.15.1)
Assembly: mm10
Supplementary files format and content: TSV (initial methylation call data)
Supplementary files format and content: BedGraph
|
| |
|
| Submission date |
Jun 20, 2022 |
| Last update date |
Sep 06, 2022 |
| Contact name |
Chan-Wang Jerry Lio |
| E-mail(s) |
[email protected]
|
| Organization name |
Ohio State University
|
| Street address |
460 W 12th Ave
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24973 |
| Series (2) |
| GSE183681 |
Epigenetic Remodeling by Vitamin C Potentiates Plasma Cell Differentiation |
| GSE206453 |
Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [Bisulfite-Seq] |
|
| Relations |
| BioSample |
SAMN29207438 |
| SRA |
SRX15797899 |
