Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Cap-H2

Cell type

Cell type Class
Cell line
Cell type
Kc167
Source
e/se
Developmental Stage
dorsal closure stage

Attributes by original data submitter

Sample

source_name
Kc167
chip antibody
CapH2
cell type
Kc167 Drosophila Embryonic Cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments. Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC. Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
14658841
Reads aligned (%)
85.8
Duplicates removed (%)
11.2
Number of peaks
4071 (qval < 1E-05)

dm6

Number of total reads
14658841
Reads aligned (%)
85.6
Duplicates removed (%)
12.4
Number of peaks
3992 (qval < 1E-05)

Base call quality data from DBCLS SRA