Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
bcd

Cell type

Cell type Class
Embryo
Cell type
1-3h embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Stage 3-5 embryos
chip antibody
House-made Bicoid antibody (Paris et al 2013)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Embryo halves were then homogenized in homogenization buffer containing 15mM NaCl, 15mM TrisHCl pH 7.5, 60mM KCl, 1mM EDTA, and 0.1% Triton-X100, with 1mM DTT, 0.1 mM PMSF, and protease inhibit cocktail (Roche) added before use. After homogenization, 0.5% NP40 was added, and following a 5 minute incubation, samples were spun down at a low speed. Nuclei in the pellet were then washed once with the homogenization buffer containing 0.2M NaCl. The low speed centrifugation was repeated, and the recovered nuclei pellet was then re-suspended in nuclear lysis buffer (10 mM TrisCl, pH 7.9, 100 mM NaCl, 1 mM EDTA, 0.5 % Sarkosyl) +1%SDS, +1.5% sarkosyl. The chromatin was recovered by spinning the sample at full speed in a micro-centrifuge at 4oC for 1 hour and was re-suspended in a small volume of nuclear lysis buffer. Chromatin was sheared to an average size of 300bp using a Covaris sonicator (peak power= 140, duty factor = 10, cycle burst = 200, time = 3 minutes). Chromatin immunoprecipitation was performed using 72ng of chromatin and 1.5ug of an anti-Bicoid polyclonal antibody described previously (Li et al., 2008). The Bicoid antibody was coupled to Dynabead M-280 sheep anti-rabbit magnetic beads and the immunoprecipitation was conducted with the standard protocol from the manufacturer. DNA libraries for the chromatin immunoprecitation samples were prepared using the Rubicon genomics thru-plex DNA-seq kit using 16 PCR cycles for posterior and whole samples and 22 cycles for anterior, middle, and input samples.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
105103288
Reads aligned (%)
8.1
Duplicates removed (%)
77.4
Number of peaks
11011 (qval < 1E-05)

dm6

Number of total reads
105103288
Reads aligned (%)
7.2
Duplicates removed (%)
79.9
Number of peaks
8476 (qval < 1E-05)

Base call quality data from DBCLS SRA