 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 27, 2017 |
| Title |
c2i_ESC_4_XX_WGBS |
| Sample type |
SRA |
| |
|
| Source name |
ES cells
|
| Organism |
Mus musculus |
| Characteristics |
passage: p3
strain: F1 (129X1/SvJ and C57BL6)
cell type: ES cells
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PureLink Genomic DNA mini kit (invitrogen) for genomic DNA
For whole genome bisulfite sequencing library, 500ng of DNA was sheared by covaris and ligated with methylated adapters supplied by TruSeqTM DNA, Sample Prep Kit-v2 (Illumina). Subsequently, DNA was bisulfite-treated using EZ DNA Methylation-Gold KitTM according to the supplier’s instruction. Final library amplification was performed using Pfu Turbo Cx (Agilent Technologies). The libraries were then sequenced on HiSeq 2500 (2 X 101 bp paired-end reads, Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
WGBS
2i-ESC #c4 XX
|
| Data processing |
Libraries were sequenced on the HiSeq2500 (2 X 101 bp or 2×100 bp paired-end reads, illumina)
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.9.1
The trimmed reads were mapped to both B6 mouse genome (mm10) and MSM/ms mouse genome independently by Bismark software-v0.15.0 with bowtie2 (version 2.2.8) and default settings, and the reads mapped to the same chromosome and positions of both B6 and MSM/ms genomes with high mapping quality (MAPQ>=20) were used for further analysis. MSM/ms mouse genome were reconstructed from mm10 using the SNPs (NIG Mouse Genome Database (MSMv4HQ, http://molossinus.lab.nig.ac.jp/msmdb/index.jsp)). Chromosomes Y and M were ommited from MSM/ms genomes because of lack of the SNPs information.
For methyl-seq libraries, the B6-derived and MSM/ms-derived sequenced reads were selected based on the MSM/ms SNPs data which were not in CpG sites and the patterns of bisulfite conversion. Methylated cytosines were extracted from the reads by the Bismark methylation extractor with --ignore 10 --ignore_r2 10 --ignore_3prime 5 --ignore_3prime_r2 5 options. For methyl-seq libraries, only the original bottom (OB) data were used for analysis of methylation status and methylation percentages were represented at the sites which have equal or more than 5 read depth.
genome build: mm10
Supplementary_files_format_and_content: bedGraph colums: <chromosome> <start position> <end position> <methylation percentage>, *The coordinates are zero-based, half-open.
|
| |
|
| Submission date |
Dec 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yasuhiro Yamada |
| E-mail(s) |
yyamada@m.u-tokyo.ac.jp
|
| Organization name |
University of Tokyo
|
| Department |
Department of Molecular Pathology
|
| Street address |
7-3-1 Hongo, Bunkyo-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-0033 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE84164 |
Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation |
| GSE84165 |
Derivation of ground-state female ESCs maintaining gamete-derived DNA methylation |
|
| Relations |
| BioSample |
SAMN06134254 |
| SRA |
SRX2416800 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2425454_c2i_ESC_4_XX.bedGraph.gz |
28.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
