Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
twi

Cell type

Cell type Class
Embryo
Cell type
Embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Oregon-R_embryo
tissue
whole-embryo
time point
02 to 04 h AEL
chip antibody
anti-Twist rabbit polyclonal, custom (Covance)
strain
Oregon R

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
21501642
Reads aligned (%)
35.3
Duplicates removed (%)
56.4
Number of peaks
16548 (qval < 1E-05)

dm6

Number of total reads
21501642
Reads aligned (%)
34.1
Duplicates removed (%)
57.8
Number of peaks
16583 (qval < 1E-05)

Base call quality data from DBCLS SRA