|
| Status |
Public on Nov 02, 2022 |
| Title |
total_LF_rep1_RNA_BS_seq |
| Sample type |
SRA |
| |
|
| Source name |
adult mouse NSCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: 6 to 8wk
tissue/cell type: adult neural stem cells from the subventricular zone (SVZ) of the lateral ventricles
genotype: WT
gender: male
|
| Growth protocol |
Adult mouse NSCs were seeded on poly-ornithine and laminin coated plates in DMEM/F12 medium (DMEM/F12, 2% B27, supplement, 2 mmol/L L-glutamine, 1x penicillin-streptomycin, 20 ng/ml epidermal growth factor (EGF, PeproTech), 20 ng/ml basic fibroblast growth factor (bFGF, PeproTech))containing Low (1.5uM), Medium (10uM) and High (80uM) folic acid for 4 days, with fresh medium change at day 2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from adult NSCs with TRIzol reagent. Polysome fractions were separated by sucrose gradient separation and polysome RNA was extracted from polysome fractions with TRIzol LS reagent following the manufacturer’s instructions. RNA samples were subject to turbo DNase digestion at 37℃ for 30min.
After two rounds of poly(A) selection, bisulfite conversion was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols
RNA BS-Seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Total poly(A) RNA
|
| Data processing |
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases
meRanGh v1.2.1 was used to map reads to C2T and G2A converted reference genomes
meRanCall was used to call m5C sites from mapped read files
In-house scripts using Python 3.9 and R 4.1.1 were used to further filter and process methylation calling files
Assembly: mm10
Supplementary files format and content: tab-delimited files containing methylation calling information for each called methylated site
|
| |
|
| Submission date |
Mar 08, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Xiguang Xu |
| E-mail(s) |
xiguang@vt.edu
|
| Organization name |
Virginia Tech
|
| Department |
Department of Biomedical Sciences and Pathobiology
|
| Lab |
Epigenomics and Computational Biology Laboratory
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE151271 |
RNA bisulfite sequencing of total and polysome RNA from adult mouse neural stem cells (NSCs) treated with 1.5uM, 10uM and 80uM folic acid for 4 days |
| GSE151726 |
Modulation of RNA cytosine-5 methylation by folate in neural stem cells |
|
| Relations |
| BioSample |
SAMN26526579 |
| SRA |
SRX14434449 |
