Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
fs(1)h

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
Dm_S2cell_Biotin_dBRD4-S_ChIPseq_GST_RNAi_IP
cell line background
S2 cells
genotype/variation
S2 stable cell line:MtnA-dBRD4-S-FLAG-Biotin
knockdown or inhibitor treatment
control RNAi (GST)
chip antibody
streptavidin T1 magnetic beads (Invitrogen 65601)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
cells were fixed for 10min in 1.8% of formaldehyde at 23 °C, nuclei were isolated, chromatin was fragmented by sonication (Covaris), The lysate was clarified by centrifugation before immunoprecipitation, and eluted by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using AMPure XP Beads (Beckman Coulter); for Rpb3 ChIP experiments Drosophila Virilis chromatin was added prior to IP as spike control. For Biotin ChIP experiments exogenous Biotin-labeled DNA fragments were added prior to IP as spike control. NEB Next Ultra II

Sequencing Platform

instrument_model
Illumina HiSeq 3000

dm3

Number of total reads
7859407
Reads aligned (%)
94.0
Duplicates removed (%)
8.7
Number of peaks
2622 (qval < 1E-05)

dm6

Number of total reads
7859407
Reads aligned (%)
93.8
Duplicates removed (%)
9.2
Number of peaks
2667 (qval < 1E-05)

Base call quality data from DBCLS SRA