Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
psq

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
cell line
Kc167
cell type
Drosophila Embryonic Cell Line
chip-antibody
Psq-M (recognizes PsqTot)
treatment
under normal conditions

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 and quenched with glycine. For ChIP-seq, nuclear lysates were sonicated to generate 200-500 bp fragments . Chromatin was precleared with Protein A or G Dynabeads at 4°C for 2 hours and incubated with antibody overnight at 4°C. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods. For HiChIP nuclei were isolated and chromatin digested by DpnII, filled in with biotin-dCTP, and ligated. After ligation, chromatin was sonicated and precleared with Protein A and G Dynabeads at 4°C for 2 hours, then precipitated using anti-CP190 or anti-Pol2phosphoSerine2 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation. For ATAC-seq Kc167 cells grown to exponential stage were treated with DMSO or triptolide as previously described. 200,000 ctrl and treated cells were collected and used for Fast-ATAC protocol. Briefly, cell pellets were resuspened in 50 µl transposes Tn5 mixture (0.01% digitonin for permeabilizing cell membrane, 2.5 µl Tn5, 25 µl TD buffer), and incubated at 30°C for 20 min with occasional shaking. After reaction, cells were cooled on ice and continued with DNA extraction by Minelute Kit (Qiagen). Libraries were constructed using the standard protocol. Genomic fragments were end repaired (NEBNext End Repair Module), A-tailed by adding adenosine to the 3' ends of fragment using Klenow fragment (3' to 5' exo minus, New England Biolabs), and adaptors were ligatedat room temperature for 1 hr with T4 DNA ligase (New England Biolabs). Libraries were amplified with Illumina primers using the KAPA SYBR FAST qPCR Master Mix.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
7655538
Reads aligned (%)
157.1
Duplicates removed (%)
13.7
Number of peaks
5229 (qval < 1E-05)

dm6

Number of total reads
7655538
Reads aligned (%)
152.0
Duplicates removed (%)
16.1
Number of peaks
4364 (qval < 1E-05)

Base call quality data from DBCLS SRA