Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Embryo
Cell type
Epiblast
NA
NA

Attributes by original data submitter

Sample

source_name
1000 E6.5 epiblasts
development stage
E6.5 embryo
ChIP
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
use microfludic chip to do DNA extraction, MNase digestion and ChIP The reagents for library preparation were provided by Illumina and were used according to the manufacturer’s protocol with appropriate modifications as described below. We purified DNA from the ChIP assay by AMPure XP beads and eluted the DNA by 20 μl Resuspension Buffer. The DNA suspension was concentrated from 20μl to 5μl by evaporation. Then, 4 μl of End Repair Mix and 1 μl Resuspension Buffer were added to the 5 μl of cleaned up DNA suspension before incubating at 30 ºC for 30 minutes and inactivating at 75 ºC for 15 minutes for end repairing. Adenylation of 3’ ends is performed by adding 8.4 μl thawed A-Tailing Mix and 1.6 μl Resuspension Buffer and incubating at 37 ºC for 30 minutes. We ligated adapters by adding 1.7 μl of DNA Ligase Mix, 3.1 μl Resuspension Buffer, and 0.2 μl Adapter Index. 30 ºC for 10 minutes is the duration for adapters ligation. We added 1 μl DNA which contains 100 ng of 5k size.= then purified DNA twice by AMPure XP Beads. Enrichment of DNA was achieved by PCR for 15 cycles. Polyacrylamide gel electrophoresis was followed another purification by AMPure XP Beads and we separated DNA with the length of 250-700bp. We extracted DNA from PAGE gel and purified it by a QIAGEN gel extraction kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
30344383
Reads aligned (%)
84.5
Duplicates removed (%)
54.7
Number of peaks
22891 (qval < 1E-05)

mm9

Number of total reads
30344383
Reads aligned (%)
84.3
Duplicates removed (%)
54.8
Number of peaks
22825 (qval < 1E-05)

Base call quality data from DBCLS SRA