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Series GSE96591 Query DataSets for GSE96591
Status Public on Aug 17, 2017
Title 2.5 dpc Uterus Chip-Seq of Kdm4a mice
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: ChipSeq allows us to identify binding sites of target proteins of interest in the genome, helping create a global profile for the same. Kdm4a is a H3K9me3 histone demethylase that acts to prevent spurious accumulation of this repressive mark at H3K4me3 positive transcription start sites. To complement transcriptome data from Kdm4a mice, we performed Chip-Seq on 2.5dpc mouse uterus of 8-10 week old littermate control and Kdm4a knockout mice for Kdm4a, H3K9me3 and H3K4me3. This would help us check which of the target genes with changed gene expression was due to the direct change in histone lanscape in absence of Kdm4a.
 
Overall design Wildtype and Kdm4a knockout mice were set up for natural timed mating. At 2.5 dpc, we harvested pre-receptive uterus from mice after confirming the presence of embryos by flushing the oviduct. The uteri were subsequently cross-linked with 1% paraformaldehyde, homogenized mechanically and chromatin extracted and sheared by sonication. 1mg for Kdm4a and 100 uG for histone IPs were used as input. ChipSeq Libraries were then constructed using Illumina from eluates using 2ng of IP-ed DNA as input material. The profiles are compared between wildtype and Kdm4a knockout conditions.
 
Contributor(s) Sankar A
Citation(s) 28827393
Submission date Mar 14, 2017
Last update date May 15, 2019
Contact name Aditya Sankar
E-mail(s) cnj376@ku.dk, aditya.sankar@embl.de
Organization name University of Copenhagen
Department Biotech Research and Innovation Centre
Lab Helin
Street address Ole Maaloes Vej 5
City Copenhagen
ZIP/Postal code 2200
Country Denmark
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (14)
GSM2536316 Kdm4a_WT1 ChIP-Seq
GSM2536317 Kdm4a_WT2 ChIP-Seq
GSM2536318 Kdm4a_KO ChIP-Seq
This SubSeries is part of SuperSeries:
GSE96686 HTS-Seq analysis of Kdm4a wildtype and knockout females at 2.5 dpc
Relations
BioProject PRJNA379111
SRA SRP101854

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE96591_RAW.tar 2.7 Gb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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