Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Kdm4a

Cell type

Cell type Class
Uterus
Cell type
Uterus
MeSH Description
The hollow thick-walled muscular organ in the female PELVIS. It consists of the fundus (the body) which is the site of EMBRYO IMPLANTATION and FETAL DEVELOPMENT. Beyond the isthmus at the perineal end of fundus, is CERVIX UTERI (the neck) opening into VAGINA. Beyond the isthmi at the upper abdominal end of fundus, are the FALLOPIAN TUBES.

Attributes by original data submitter

Sample

source_name
Uterus
strain
C57BL6
genotype/variation
WT
Stage
2.5 dpc
antibody
Anti-Jmjd2a (Cell Signaling; Catalog Nr #5328)
antibody amount
5ug
tissue
Uterus
input amount
Chromatin (1mg)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
At 2.5 dpc (days post coitus), females were sacrificed and checked for presence of preimplantation embryos by flushing the oviduct. Whole uterus were immediately cleaned of fat and cut into halves and pieces from each female were cross linked with 1% paraformaldehyde in PBS at room temperature for 10 minutes. Then, they were placed in 0.125 M glycine for 5 minutes to stop cross-linking. Subsequently, samples were washed in cold PBS twice and then homogenized to single cells using mechanical shearing of tissue in lysis buffer without detergent (SDS). Cells were pellleted at 1200 rpm for 5 minutes and then supernatant aspirated. Pellet was resuspended in lysis buffer with detergent (SDS) to release chromatin for 10 minutes at room temperature. Loose chromatin was pelleted at 1500 rpm for 5 minutes and supernatant discarded. Pellet was resuspended in ice-cold sonication buffer and subjected to sonication using Diagenode Picoruptor. Sonication efficiency is checked on 1% agarose gel upon decrosslinking and sheared chromatin is obtained by spinning at 20000G/4C/15 mins to pellet down non-chromatin fragments. Pure chromatin is measured for protein concentration and stored at -80 C till immunoprecipitation. Protocol followed manufacturers instructions for ChiPSeq libraries using the NEBNext Ultra II DNA library prep kit (Illumina, #E7645)

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
20764621
Reads aligned (%)
78.6
Duplicates removed (%)
16.7
Number of peaks
298 (qval < 1E-05)

mm9

Number of total reads
20764621
Reads aligned (%)
78.4
Duplicates removed (%)
16.7
Number of peaks
271 (qval < 1E-05)

Base call quality data from DBCLS SRA