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Sample GSM1695384 Query DataSets for GSM1695384
Status Public on Aug 27, 2015
Title H3k4me3 Eye ChIPSeq
Sample type SRA
 
Source name 100 eyes from E10.5 mouse embryos
Organism Mus musculus
Characteristics tissue: eye
developmental stage: 10.5E
strain: C57/BL6
antibody: Antibody pAB-030-050 Diagenode
Extracted molecule genomic DNA
Extraction protocol 100 eyes from E10.5 mouse embryos were pooled and chromatin was cross-linked with 1% formaldehyde for 15 min and fragmented to obtain DNA in the range of 200–500 bp. DNA was divided in two pools (10mg) and precipitated with 2mg anti-H3K4me1 (CS-037-100, Diagenode) and anti-H3K4me3 (pAB-030-050 Diagenode)
Libraries were prepared for sequencing using standard Illumina protocols for genomic DNA
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description wildtype
Data processing libraries sequenced usign Illumina GAIIx single end 49nt
base-calling was produced by Illumina RTA Software v 1.13.48
demultiplexed fastq files were generated using CASAVAv1.7
reads were trimmed to 36nt using cutadapt v1.7.1
36nt reads were mapped to mouse genome using BWA v0.7.10 with default aln options
Duplicate Reads have been removed using Picard tools v1.97(1540)
Peak Calling was perform with HOTSPOT v4.1.0 using a random simulated Input to calculate FDR
Peaks selected at FDR 0.01
Genome_build: mm9
Supplementary_files_format_and_content: peaks selected at FDR 0.01 in bed format
 
Submission date May 26, 2015
Last update date May 15, 2019
Contact name Carlos Torroja
E-mail(s) ctorroja@cnic.es
Phone (+34) 91 4531200
Organization name Centro Nacional de Investigaciones Cardiovasculares (CNIC)
Department Bioinformatics Unit
Street address Melchor Fernandez Almagro, 3
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL17021
Series (1)
GSE62786 Meis1 coordinates a network of genes implicated in eye development and microphthalmia
Relations
BioSample SAMN03734273
SRA SRX1038028

Supplementary file Size Download File type/resource
GSM1695384_H3k4me3EyeChIP_mm9_Peaks.bed.gz 328.0 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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