Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
E(z)

Cell type

Cell type Class
Embryo
Cell type
12-24h embryos
NA
NA

Attributes by original data submitter

Sample

source_name
Drosophila embryo
strain
Bloomington stock strain 9736
tissue
Developmental Stage Embryo 12-24h
age
Embryo 12-24h
antibody
BioTAP-N-E(z)
genotype
y[1] w[1118]; PBac{y[+]-attP-9A [mw+]BioTAP-N-Ez}VK00018

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
We followed the BioTAP-XL protocol as described in (Alekseyenko et al. 2015). In brief, embryos of BioTAP transgenic fly lines (Pc-C-BioTAP, BioTAP-N-E(z) and BioTAP-N-Scm) were collected between 12 and 24 h after fertilization and were stored for up to 3 days at 4°C. Every 3 days, embryonic nuclei were crosslinked and extracts were prepared as described, snap-frozen with liquid nitrogen and stored at -80°C. These steps were repeated until extracts from ~50g embryos were pooled. Stable S2 cell lines expressing BioTAP transgenes (Pc-C-BioTAP and BioTAP-N-Scm) were incubated in four 2.8L Fernbach glass flasks at 26.5 °C and 90 rpm. In each flask, cells were grown in 500ml of HyClone CCM3 serum-free media to a density of ~1x107 cells/ml. Crosslinked nuclear extracts from S2 cell lines were prepared from ~2x1010 cells grown in four flasks. After sonication, tandem affinity purification was performed to isolate the BioTAP-tagged bait along with its protein interaction partners and associated genomic DNA. Interacting proteins were identified by on-bead trypsinization of bound complexes followed by liquid chromatography mass-spectrometry (LC-MS/MS) of the resulting peptides. Libraries for sequencing were prepared using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

dm3

Number of total reads
14989551
Reads aligned (%)
96.6
Duplicates removed (%)
7.4
Number of peaks
1909 (qval < 1E-05)

dm6

Number of total reads
14989551
Reads aligned (%)
96.3
Duplicates removed (%)
8.4
Number of peaks
1649 (qval < 1E-05)

Base call quality data from DBCLS SRA