title: GSM1616471: Pc-C-BioTAP_input_emb_replicate2; Drosophila melanogaster; ChIP-Seq
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.
identifiers.namespace: GEO
identifiers.id: GSM1616471