|
| Status |
Public on Jun 27, 2019 |
| Title |
WGBS: BS_diff63_ctr_d9_3 |
| Sample type |
SRA |
| |
|
| Source name |
BS-seq control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: LUHMES-derived neurons
div: Day 9
passage: 15-20
cell type: LUHMES cell line
differentiation: differentiation 63
|
| Growth protocol |
LUHMES cells were cultured and differentiated according to published protocol (Shah et al., 2016).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, genomic DNA was isolated using DNeasy Blood and Tissue kit (Qiagen) according to manufacturer’s procedure. The bisulfite reaction was performed using EZ DNA Methylation Gold kit on 100 ng of gDNA according to manufacturer protocol. Genomic DNA was mixed with 0.5% of unmethylated lambda DNA (Promega) for assessment of efficiency of bisulfite reaction. For TAB-seq, the TAB reaction was performed according to published protocol and genomic DNA was sonicated for 30 cycles of 30 sec ON and 30 sec OFF on low power using a Bioruptor (Diagenode). Ox-BS was prepared by CEGX company using TrueMethyl kit workflow.
For WGBS, random primed DNA synthesis and tagging was performed on converted gDNA. Finally, DNA was PCR amplified to generate a library for high-throughput sequencing. For TAB-seq, DNA was end-repaired and the ends where 3’ adenylated in order to facilitate adapter ligation. Size selection was performed using Agencourt AMPure XP (Beckman Coulter) beads and, after adapter ligation and size selection, DNA was bisulfite treated using EpiTect Bisulfite kit (Qiagen) and PCR amplified using custom primers
WGBS of wildtype LUHMES-derived neurons at day 9 was performed by whole genome bisulfite sequencing using an Epignome Methyl-seq kit (Epicentre, Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trim reads with trimmomatic v0.32
Align reads with Bismark v0.19
Deduplicate reads (Bismark)
Extract Methylation values (Bismark)
Genome_build: hg19
Supplementary_files_format_and_content: Bismark .cov format
|
| |
|
| Submission date |
Feb 15, 2019 |
| Last update date |
Jun 27, 2019 |
| Contact name |
Shaun Michael Webb |
| E-mail(s) |
shaun.webb@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
2.21 Swann Building, Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE125660 |
Study of MeCP2 in LUHMES-derived neurons |
| GSE126639 |
Study of DNA methylation pattern in single basepair resolution in the human dopaminergic neurons |
|
| Relations |
| BioSample |
SAMN10954145 |
| SRA |
SRX5383164 |
