|
| 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) |
[email protected]
|
| 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 |
