Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
msl-2

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
S2 cell line
cell line
S2
chip antibody
MSL2
treatment
MLE RNAi

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP DNA; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. 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; cells were crosslinked in growth medium using 1% formaldehyde for 60 minutes in icewater. Fixation was quenched by addition of glycine to a final concentration of 125 mM. After washing, cells were resuspended in RIPA buffer and sonciated using a Covaris S220 (PIP 100 W, DF 20%, 200 CB for 30 min) to generate 180-bp chromatin fragments. 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
56185355
Reads aligned (%)
89.4
Duplicates removed (%)
56.9
Number of peaks
5990 (qval < 1E-05)

dm6

Number of total reads
56185355
Reads aligned (%)
89.0
Duplicates removed (%)
59.4
Number of peaks
4713 (qval < 1E-05)

Base call quality data from DBCLS SRA