|
| Status |
Public on Sep 06, 2022 |
| Title |
Naive_B_rep1_5hmC |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: B cell
treatment: Unstimulated
sample type: 5hmC-pulldown
|
| 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.
DNA was quantified with Qubit (ThermoFisher) and sonicated to around 150-200bp using Bioruptor Pico (Diagenode). 5hmC enrichment analysis was performed using the HMCP kit (Cambridge Epigenetix) based on the addition of azido-glucose to 5hmC by T4-beta-glucosyltransferase following the manufacturer’s instruction.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: 5hmC
Bowtie2 (v2.4.2)
Samtools (v1.10)
Deeptools (v3.5.1)
HOMER (v4.8)
DiffBind (v2.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Txt (peaks), Bigwig
|
| |
|
| Submission date |
Sep 08, 2021 |
| Last update date |
Sep 06, 2022 |
| Contact name |
Chan-Wang Jerry Lio |
| E-mail(s) |
lio.4@osu.edu
|
| Organization name |
Ohio State University
|
| Street address |
460 W 12th Ave
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE183679 |
Vitamin C Potentiates Plasma Cell Differentiation via TET-mediated DNA modification [5hmC] |
| GSE183681 |
Epigenetic Remodeling by Vitamin C Potentiates Plasma Cell Differentiation |
|
| Relations |
| BioSample |
SAMN21185322 |
| SRA |
SRX11989886 |
