Curated Sample Data


Genome
dm3
Antigen Class
Histone
Antigen
H4K5ac
Cell type Class
Embryo
Cell type
Mitotic cycle 14

Cell type information


NA
NA

Attributes by Original Data Submitter


source_name
embryos, cycle 14a, H4K5ac ChIP
strain/background
Oregon R
genotype/variation
wild-type
tissue
embryo
developmental stage
mitotic cycle 14(a-b)
chip antibody
anti-H4K5ac (Millipore, 07-327, lot 1911263)

Metadata from Sequence Read Archive

Library Description


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.

Platform Information


instrument_model
Illumina HiSeq 2000

External Database Query

Logs in read processing pipeline


Number of total reads
24054255
Reads aligned (%)
28.5
Duplicates removed (%)
15.3
Number of peaks
1410 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA