|
| Status |
Public on Feb 15, 2012 |
| Title |
F1i_ChIP_Seq_input |
| Sample type |
SRA |
| |
|
| Source name |
Frontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue: frontal cortex
strain: 129X1/SvJ x Cast/EiJ
chip-antibody: none
|
| 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 |
Frozen mouse frontal cortex from the F1 crosses was thawed on ice and processed with a razor blade into small pieces. Tissue was then crosslinked with formaldehyde, washed, homogenized, and proceeded for ChIP. To isolate chromatin, formaldehyde-cross-linked nuclei were sonicated using a Branson 450 Sonifier (Branson, Danbury, CT). ChIP DNA was subjected to end repair, A-tailing, adaptor ligation, and gel purification. Following PCR amplification for 18 cycles, the final libraries were subjected to sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing reads for the ChIP-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 |
Jun 29, 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 |
| SRA |
SRX081822 |
| BioSample |
SAMN00632069 |
| Named Annotation |
GSM751471_F1i_ChIP_Seq_input_129.bed.gz |
| Named Annotation |
GSM751471_F1i_ChIP_Seq_input_Cast.bed.gz |
| Named Annotation |
GSM751471_F1i_ChIP_Seq_input_total.bed.gz |
