|
| Status |
Public on Feb 15, 2012 |
| Title |
F1i_MethylC_Seq |
| Sample type |
SRA |
| |
|
| Source name |
Frontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: frontal cortex
strain: 129X1/SvJ x Cast/EiJ
|
| 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 |
Five µg of genomic DNA was extracted from the frontal cortex of the F1 crosses and was spiked in with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented by sonication to 100-600 bp. Purified DNA fragments were end-repaired and ligated to paired-end cytosine- methylated adapters provided by Illumina. Size-selected adapter-ligated DNA was treated with sodium bisulfite using the EZ DNA methylation-Gold Kit (Zymo Research). The resulting DNA molecules were enriched by PCR, purified and sequenced following standard protocols from Illumina. The average insert sizes of the paired-end libraries are 140bp and 143bp, with the standard deviation of 47bp and 49bp, for the F1i and F1r strains, respectively.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
MethylC-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. PCR duplicates for each library were removed with the Picard program(Picard 2011).
|
| |
|
| Submission date |
Jul 01, 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 |
GPL13112 |
| Series (2) |
| GSE30199 |
Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (ChIP-seq and Methyl-seq) |
| GSE33722 |
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation |
|
| Relations |
| Reanalyzed by |
GSE77019 |
| SRA |
SRX081824 |
| SRA |
SRX081825 |
| SRA |
SRX081826 |
| BioSample |
SAMN00632071 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM753569_F1i_MethylC_Seq_129_crick.bam |
11.3 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_MethylC_Seq_129_watson.bam |
11.3 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_MethylC_Seq_Cast_crick.bam |
10.0 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_MethylC_Seq_Cast_watson.bam |
10.3 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_MethylC_Seq_unassigned_crick.bam |
36.0 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_MethylC_Seq_unassigned_watson.bam |
37.5 Gb |
(ftp)(http) |
BAM |
| GSM753569_F1i_mC_crick.txt.gz |
2.4 Gb |
(ftp)(http) |
TXT |
| GSM753569_F1i_mC_watson.txt.gz |
2.4 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
