Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
bcd

Cell type

Cell type Class
Embryo
Cell type
Blastoderm
NA
NA

Attributes by original data submitter

Sample

source_name
Blastoderm embryos
developmental stage
Blastoderm
strains
Oregon R
chip antibody
Bicoid (Li et al. 2008)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was isolated by CsCl gradient ultracentrifugation, fragmented and immunoprecipitated with affnity-purified antibody Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly DNA fragments were converted to phosphorylated blunt ends using T4 DNA polymerase, Klenow DNA polymerase, and T4 polymerase kinase, a 3' A base overhang was added using Klenow DNA polymerase exo- (3' to 5' exo minus), and Illumina adapters were ligated to the fragments. We carried out the PCR step for enrichment of adapter-modified DNA prior to the library size selection, and limited the amplification to 15 cycles. After the amplification step, we size-selected DNA fragments of 150-250 bp.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

dm3

Number of total reads
8416225
Reads aligned (%)
67.9
Duplicates removed (%)
14.1
Number of peaks
1111 (qval < 1E-05)

dm6

Number of total reads
8416225
Reads aligned (%)
65.4
Duplicates removed (%)
16.9
Number of peaks
1773 (qval < 1E-05)

Base call quality data from DBCLS SRA