 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 31, 2017 |
| Title |
Control #2 WGBS |
| Sample type |
SRA |
| |
|
| Source name |
Control, day ~105 conceptus
|
| Organism |
Bos indicus x Bos taurus |
| Characteristics |
tissue: fetal skeletal muscle
condition: Control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA were isolated using the phenol-chrolorform method
For whole genome bisulfite sequencing (WGBS) library preparation, 1μg bovine DNA was subject to sodium bisulfite mutagenesis using NEB EpiMark Bisulfite Conversion Kit (NEB E3318) according to the manufacturer’s instructions. Prior to the sodium bisulfite reaction, 5ng (0.5%) unmethylated cl857 Sam7 Lambda DNA (48,502bp, Promega D1521) was combined with bovine DNA to act as an internal control to monitor the bisulfite conversion rate. The WGBS libraries were generated using the NEBNext Ultra DNA library Prep Kit for Illumina (NEB E7370) as per the manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Day ~105 Bos indicus taurus × Bos taurus taurus F1 fetal skeletal muscle
|
| Data processing |
The Cutadapt program (version: 1.9.1) was used to remove the adaptor sequences in the read pairs. For base quality trimming, DynamicTrim (version 3.1) was used to obtain the longest segment of the read in which each base has <1% error rate.
WGBS read pairs were aligned to the bovine reference genome assembly UMD3.1 and the Lambda genome using Bismark (version: 0.15.0) with default parameters. Only uniquely aligned read pairs that had the expected read mate orientation and expected ranges of insert size were retained for further analyses.
Bis-SNP (version: 0.82.2) was used to perform the SNP calling using the WGBS data. Only CpG site that show consensus CpG context for both parental alleles (i.e., do not overlap any SNPs identified by Bis-SNP) were used for the subsequent analyses.
As CpG methylation is symmetric, the methylation level was determined using the reads from both forward and reverse strands covering the same symmetric CpG site. The methylation level was calculated as: (number of “C” reads)/(number of “C” reads + number of “T” reads).
For most analyses, only CpGs covered by at least by five reads were used for the calculation of the methylation level. The exception is the allele-specific methylation analyses, in which only CpGs covered at least by 8 reads (four reads per parental allele) were included for the statistical test. For reads with PCR duplicates, only one of them was randomly choosed for the determination of the methylation level.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Bigwig files were generated using "bedGraphToBigWig" from UCSC genome browser. Scores represent the ratios of methylated CpGs except for the "Fisher_exact_test_p-value.bw" which represent the significance of allele-sepcific DNA methylation
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rocío Melissa Rivera |
| E-mail(s) |
riverarm@missouri.edu
|
| Organization name |
University of Missouri, Columbia
|
| Department |
Animal Sciences
|
| Street address |
920 East Campus Drive, ASRC 164
|
| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL22942 |
| Series (1) |
| GSE93775 |
Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome |
|
| Relations |
| BioSample |
SAMN06238127 |
| SRA |
SRX2500404 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2461854_Control__2_CpG_methylation.bw |
211.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
