|
| Status |
Public on Oct 03, 2016 |
| Title |
PBAT_MERVL+Zscan4+_to_Neg_72h_A |
| Sample type |
SRA |
| |
|
| Source name |
PBAT MERVL+Zscan4+ to Neg 72h A
|
| Organism |
Mus musculus |
| Characteristics |
cell line: E14 embryonic stem cell
strain: C57BL/6 wild-type
|
| Treatment protocol |
Either 72 hours or 7 days culture time before first and second sorts
|
| Growth protocol |
Steady state MERVL+Zscan4c+ ESCs were sorted using the fluorescent reporters. The cells were then returned to culture and the newly emerging negative cells sorted after 72 hours or 7 days for bisulfite analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole genome bisulfite sequencing libraries were generated using the PBAT method as per Peat et al. 2014 Cell Reports using 10 cycles of PCR
BS-Seq (PBAT)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
BS-Seq (PBAT): Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1, parameters: --paired). Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to use overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.14.4 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults. Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
Genome_build: GRCm38
Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome> <position> <strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context>
|
| |
|
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Richard Andrews |
| E-mail(s) |
[email protected]
|
| Phone |
+441223496000
|
| Organization name |
The Babraham Institute
|
| Department |
Science Services
|
| Lab |
Bioinformatics
|
| Street address |
Babraham Research Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE85776 |
MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs |
|
| Relations |
| BioSample |
SAMN05589744 |
| SRA |
SRX2034572 |
