|
| Status |
Public on Feb 15, 2012 |
| Title |
F1r_FspEI_Seq |
| Sample type |
SRA |
| |
|
| Source name |
Frontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: Cast/EiJ x 129X1/SvJ
gender: male
tissue: frontal cortex
|
| Growth protocol |
The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories (http://jaxmice.jax.org/) and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
A total of 500ng genomic DNA isolated from IMR90, MEF, and the frontal cortex of F1i and F1r was digested in parallel by the DNA methylation dependent restriction enzyme FspEI. FspEI recognizes the CmC site (the second cytosine is methylated and can be in the context of CG, CHG or CHH) and creates a 5’ protruding end 17 bases downstream of the methylcytosine. A similar experiment was performed by incubating the F1i genomic DNA with a DNA methylation independent restriction enzyme BstNI. The digested DNA was gel purified, size selected for fragments within 100-600bp. The resulting DNA was then prepared as genomic DNA libraries for high-throughput sequencing (Illumina).
|
| |
|
| Library strategy |
MRE-Seq |
| Library source |
genomic |
| Library selection |
Restriction Digest |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
FspEI-Seq reads were mapped using Novoalign (Novocraft, Malaysia) with adapter sequences stripped. Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads) that particularly benefits sequencing read mapping around SNPs and indels. Only reads that were perfectly mapped were used to determine the positions of methylcytosines on the same strand.
|
| |
|
| Submission date |
Nov 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei@ucsd.edu
|
| Organization name |
UCSD
|
| Street address |
9500 Gilman Dr. CMM East, Room 2071
|
| City |
San Diego |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE33579 |
Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (MRE-seq) |
| GSE33722 |
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation |
|
| Relations |
| SRA |
SRX107372 |
| BioSample |
SAMN00760461 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM830151_F1r.FspEI.129.bam |
100.4 Mb |
(ftp)(http) |
BAM |
| GSM830151_F1r.FspEI.129.crick.mC.txt.gz |
731.1 Kb |
(ftp)(http) |
TXT |
| GSM830151_F1r.FspEI.129.watson.mC.txt.gz |
733.7 Kb |
(ftp)(http) |
TXT |
| GSM830151_F1r.FspEI.Cast.bam |
97.5 Mb |
(ftp)(http) |
BAM |
| GSM830151_F1r.FspEI.Cast.crick.mC.txt.gz |
675.2 Kb |
(ftp)(http) |
TXT |
| GSM830151_F1r.FspEI.Cast.watson.mC.txt.gz |
676.7 Kb |
(ftp)(http) |
TXT |
| GSM830151_F1r.FspEI.bam |
820.3 Mb |
(ftp)(http) |
BAM |
| GSM830151_F1r.FspEI.crick.mC.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
| GSM830151_F1r.FspEI.unassigned.bam |
649.1 Mb |
(ftp)(http) |
BAM |
| GSM830151_F1r.FspEI.watson.mC.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
