|
| Status |
Public on Oct 03, 2023 |
| Title |
cR_H9_EOS_d0_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
chemically reset cR-H9-EOS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: chemically reset cR-H9-EOS
cell type: chemically reset hPSC
day of_formative_transition: 0
biological replicate: 3
culture condition: N2B27 and 2uM XAV939
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
Post-bisulfite adaptor-tagging libraries for whole-genome DNA methylation analysis were prepared from purified genomic DNA as previously described (von Meyenn et al., 2016; Miura et al., 2012; Smallwood et al., 2014). PBAT libraries were prepared by bisulfite converting Proteinase K digested cell lysates using the EZ DNA Methylation-Direct Kit (Zymo). After cleanup, 1st strand synthesis was performed using 6N-forward oligos at 37°C for 90 minutes. Subsequently, samples were treated with Exonuclease I for 1 hour at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligos and incubated at 37°C for 90 minutes. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. Paired-end sequencing was carried out on HiSeq 2500 instruments (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
PBAT
|
| Data processing |
nf-core/methylseq v1.4 pipeline used to process the data
Bismark genomePrep v0.22.2 used for bisulfite genome preparation
FastQC v0.11.8 used for quality control
TrimGalore v0.6.4 used for trimming low quality bases + adapter sequences
Bismark v0.22.2 with HISAT2 v2.1.0 used for read mapping
Bismark Deduplication v0.22.2 used to remove alignments with identical mapping position
Bismark methXtract v0.22.2 used to generate the cytosine methylation calls
Assembly: hg38
Supplementary files format and content: Bismark CpG coverage report files tab-delimited with 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>
|
| |
|
| Submission date |
Nov 21, 2022 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Laura Biggins |
| E-mail(s) |
laura.biggins@babraham.ac.uk
|
| Organization name |
The Babraham Institute
|
| Department |
Bioinformatics
|
| Street address |
Babraham Research Campus
|
| City |
Cambridge |
| ZIP/Postal code |
CB22 3AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE218511 |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells [PBAT] |
| GSE218512 |
Epigenetic dynamics during capacitation of naïve human pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN31825780 |
| SRA |
SRX18337792 |
