Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Hmr

Cell type

Cell type Class
Larvae
Cell type
L2-4
NA
NA

Attributes by original data submitter

Sample

source_name
whole cell
cell line
L2-4
treatment
dCenpC RNAi
ChIP
HMR (Thomae et al, 2013)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChiP is prefromed exactly as described in Gerland et al, 2017. Shortly, the cells were crosslinked in 1% FA for 5 min at room temperature and frozen. Chromatin from 50 million cells was sheared in TE/0.1%SDS, the buffer was adjusted to RIPA and after preclearing the sheared extract and taking 1/10 as an input, IP was done overnight. Beads were washed, after which RNA/protein digestion and decrosslinking was performed. DNA was purified using AMPure XP beads. Libraries were prepared from 1 ng DNA with Microplex Diagenode kit, according to manufacture's instructions, without size selection.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

dm3

Number of total reads
24131564
Reads aligned (%)
94.4
Duplicates removed (%)
16.4
Number of peaks
6041 (qval < 1E-05)

dm6

Number of total reads
24131564
Reads aligned (%)
94.1
Duplicates removed (%)
19.3
Number of peaks
5357 (qval < 1E-05)

Base call quality data from DBCLS SRA