Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
dl

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Dorsal ChIP-seq (Drosophila embryos) Rep 1
tissue
whole-embryo
time point
02 to 04 h AEL
chip antibody
anti-Dorsal rabbit polyclonal, custom (GenScript)
strain
Oregon R
multiplex barcode
ACAGTG

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
embryos were cross-linked in 1.8% formaldehyde. Embryos were then dounced to break down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~100 mg embryos was used DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
16955196
Reads aligned (%)
71.6
Duplicates removed (%)
20.0
Number of peaks
14949 (qval < 1E-05)

dm6

Number of total reads
16955196
Reads aligned (%)
68.9
Duplicates removed (%)
22.8
Number of peaks
16315 (qval < 1E-05)

Base call quality data from DBCLS SRA