Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nup98-96

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
Nup98

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. 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. 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
30146221
Reads aligned (%)
89.2
Duplicates removed (%)
41.3
Number of peaks
10417 (qval < 1E-05)

dm6

Number of total reads
30146221
Reads aligned (%)
85.7
Duplicates removed (%)
43.5
Number of peaks
8280 (qval < 1E-05)

Base call quality data from DBCLS SRA