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Sample GSM751472 Query DataSets for GSM751472
Status Public on Feb 15, 2012
Title F1r_ChIP_Seq_input
Sample type SRA
Source name Frontal cortex
Organism Mus musculus
Characteristics tissue: frontal cortex
strain: Cast/EiJ x 129X1/SvJ
chip-antibody: none
Growth protocol The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories ( 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
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
SRA SRX081823
BioSample SAMN00632070
Named Annotation GSM751472_F1r_ChIP_Seq_input_129.bed.gz
Named Annotation GSM751472_F1r_ChIP_Seq_input_Cast.bed.gz
Named Annotation GSM751472_F1r_ChIP_Seq_input_total.bed.gz

Supplementary file Size Download File type/resource
GSM751472_F1r_ChIP_Seq_input_129.bed.gz 239.6 Mb (ftp)(http) BED
GSM751472_F1r_ChIP_Seq_input_Cast.bed.gz 222.6 Mb (ftp)(http) BED
GSM751472_F1r_ChIP_Seq_input_total.bed.gz 1.0 Gb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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