Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
vtd

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
ChIP-seq after 3 hours Flv treatment
cell line
Kc167
cell type
Embryonic Cell Line
treatment
3 hours Flv treatment
chip-antibody
Rad21

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-RNAPII or anti-Rad21 antibody overnight. Isolated chromatin was washed, eluted, reverse crosslinked and purified by standard methods, after which ligation events were enriched by streptavidin precipitation. Libraries were constructed using the standard protocol for ChIP-seq and Hi-C or using a Tn5 library prepartion protocol for HiChIP. Genomic fragments were end repaired, 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). For Tn5 protocol samples were incubated with Tn5 transposase in the presence of adaptors. 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
21361239
Reads aligned (%)
91.8
Duplicates removed (%)
16.5
Number of peaks
5380 (qval < 1E-05)

dm6

Number of total reads
21361239
Reads aligned (%)
91.2
Duplicates removed (%)
18.1
Number of peaks
3338 (qval < 1E-05)

Base call quality data from DBCLS SRA