Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
msl-2

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
Kc cell line
cell line
Kc
chip antibody
MSL2
RNAi
SXL construct 1
days of treatment
6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. Chromatin was precleared using a protein A/protein G-sepharose mixture for 1 hr at 4°C. 200 µl chromatin was incubated with appropriate amounts of antibodies in a total volume of 500 µl RIPA buffer at 4°C over night. After washing and crosslink revearsal, immunprecipitated nucleic acids were purified on GFX columns (GE Healthcare). Input DNA; 40 million cells were re-suspended in ice-cold homogenization buffer and fixed with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine (final) the cells were collected and washed three-times with ice-cold RIPA buffer. Fixed nuclei were sonicated in RIPA buffer with a Covaris sonifier (PIP: 140, DF 20%, CB: 200) for 30 minutes. After crosslink revearsal, nucleic acids were purified on GFX columns (GE Healthcare). The Diagenode MicroPlex library kit was used to prepare libraries from 1-2ng of either input or DIP DNA quantified using the Qubit® dsDNA HS Assay kit (Life Technologies Q32851)

Sequencing Platform

instrument_model
Illumina HiSeq 1500

dm3

Number of total reads
22849299
Reads aligned (%)
61.5
Duplicates removed (%)
29.3
Number of peaks
2851 (qval < 1E-05)

dm6

Number of total reads
22849299
Reads aligned (%)
55.7
Duplicates removed (%)
25.3
Number of peaks
1198 (qval < 1E-05)

Base call quality data from DBCLS SRA