Curated Sample Data


Genome
dm3
Antigen Class
Input control
Antigen
Input control
Cell type Class
Cell line
Cell type
S2-DRSC

Cell type information


Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by Original Data Submitter


source_name
S2 cells (male embryo-derived cell line)
strain
S2-DRSC
tissue
Embryo-derived cell-line
age
Late embryonic stage
antibody
none
genotype
wildtype S2 cells, co-transfected with pFly-BioTAP-N-Scm and pHygro (for selection)

Metadata from Sequence Read Archive

Library Description


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.

Platform Information


instrument_model
Illumina HiSeq 2500

External Database Query

Logs in read processing pipeline


Number of total reads
26721750
Reads aligned (%)
1.1
Duplicates removed (%)
81.2
Number of peaks
141 (qval < 1E-05)

Sequence Quality Data from DBCLS SRA