|
| Status |
Public on Apr 26, 2024 |
| Title |
WGBS_MECP2_WT_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
neuron
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuron
cell line: hES-neurons
cell type: neuron
genotype: WT MECP2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three-week differentiated endogenous-tagged WT MECP2-GFP NGN2-neurons were collected for the genomic DNA extraction using the Quick-gDNA MicroPrep (Zymo D3020). Bisulfite conversion and library preparation were performed using Pico Methyl-Seq Library Prep Kit (Zymo D5455) according to the manufacturer’s instructions. Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) on a paired-end 100x100 run with ~650-800 million reads.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Whole genome bisulfite sequencing of hESC derived neurons with WT MECP2
|
| Data processing |
For WGBS data, adapters were trimmed with Trim Galore! (v0.6.7), and reads were mapped to the bisulfite-prepared canonical chromosomes of the human genome (GRCh38/hg38) with bismark (v0.22.3) and deduplicated. The methylation status of each cytosine of each read was assayed with bismark_methylation_extractor, and methylation fraction and read coverage at each position were calculated with the bedtools suite (v2.29.2). Cytosines were partitioned into CpG and mCA contexts, and any sites with read coverage less than 5 were removed. The bedtools suite was used to further mean-summarize methylation fraction across genome features.
Assembly: hg38
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Mar 13, 2024 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Yi Liu |
| E-mail(s) |
yiliu@wi.mit.edu
|
| Phone |
6173010107
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Jaenisch lab
|
| Street address |
455 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE230715 |
MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons [WGBS] |
| GSE230716 |
MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons |
|
| Relations |
| BioSample |
SAMN40438294 |
| SRA |
SRX23939109 |
