Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Embryo
Cell type
Mitotic cycle 11-13
NA
NA

Attributes by original data submitter

Sample

source_name
embryos, cycle 12, H3K27me3 ChIP
strain/background
Oregon R
genotype/variation
wild-type
tissue
embryo
developmental stage
mitotic cycle 11-13
chip antibody
anti-H3K27me3 (Millipore, 07-449, lot JBC1873477)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
7.5, 0.7, 0.4, and 0.3 g of embryos at four different stages, respectively, were used to prepare chromatin for immunoprecipitation following the CsCl2 gradient ultracentrifugation protocol as previously described (Harrison et al., 2011).The chromatin obtained was fragmented to sizes ranging from 100 to 300 bp using a Bioruptor (Diagenode, Inc.) for a total processing time of 140 min (15 s on, 45 s off), with power setting at "H". Prior to carrying out chromatin immunoprecipitation, we mixed the chromatin from each sample with a roughly equivalent amount of chromatin isolated from stage 5 (mitotic cycle 14) D. pseudoobscura embryos, and used about 2 µg of total chromatin (1 µg each of the D. melanogaster and D. pseudoobscura chromatin) for each chromatin immunoprecipitation. The chromatin immunoprecipitation reactions were carried out as described previously (Harrison et al., 2011) with 0.5 ug anti-H4K5ac (Millipore, 07-327), 0.5 ug anti-H3K4me3 (Abcam, ab8580), 0.5 ug anti-H3K27ac (Abcam, ab4729), 1 ug anti-H3 (Abcam, ab1791), 0.75 ug anti-H3K4me1 (Abcam, ab8895), 0.75 ug anti-H4K8ac (Abcam, ab15823), 1.5 ul anti-H3K9ac (Activemotif, 39138), 0.75 ug anti-H3K18ac (Abcam, ab1191), 3 ug anti-H3K27me3 (Millipore, 07-449), or 0.75 ug anti-H3K36me3 (Abcam, ab9050). The sequencing libraries were prepared from the ChIP and Input DNA samples using the Illumina TruSeq DNA Sample Preparation kit following the manufacturer's instructions, and DNA was subjected to ultra-high-throughput sequencing on Illumina HiSeq 2000 DNA sequencers. The libraries were combined into pools, with each containing 6-8 libraries with different index and at similar concentrations, and each library pool was sequenced (100 bp single-end read) in a single lane in a flow cell.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm6

Number of total reads
21733577
Reads aligned (%)
26.5
Duplicates removed (%)
75.3
Number of peaks
1362 (qval < 1E-05)

dm3

Number of total reads
21733577
Reads aligned (%)
26.7
Duplicates removed (%)
71.2
Number of peaks
1096 (qval < 1E-05)

Base call quality data from DBCLS SRA