Comment[ArrayExpressAccession] E-MTAB-1511 MAGE-TAB Version 1.1 Investigation Title Evolutionary comparison of CTCF and YY1 binding in primate lymphoblastoid cell lines Comment[Submitted Name] Evolutionary comparison of CTCF and YY1 binding in primate lymphoblastoid cell lines Experiment Description We performed an evolutionary comparison of the binding of the TF CTCF in human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines (LCLs). We also probes YY1 binding in human, chimpanzee, orang-utan and baboon LCLs as well as human and mouse liver. Experimental Design species_design in_vitro_design in_vivo_design replicate_design ChiP-seq Comment[AEExperimentType] ChIP-seq Comment[AEExperimentDisplayName] ChIP-seq of human, chimpanzee, gorilla, orang-utan, macaque, baboon and marmoset using lymphoblastoid cell lines to investigate the evolutionary comparison of CTCF and YY1 binding Experimental Factor Name Organism IMMUNOPRECIPITATE Experimental Factor Type Organism immunoprecipitate Quality Control Type biological_replicate technical_replicate Public Release Date 2013-11-20 Person Last Name Schwalie Person First Name Petra Catalina Person Mid Initials Person Email petra.schwalie@epfl.ch Person Phone Person Address Person Affiliation EFPL Person Roles submitter PubMed ID 24380390 Publication Author List Schwalie PC, Ward MC, Cain CE, Faure AJ, Gilad Y, Odom DT, Flicek P Publication Title Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes Publication Status submitted Protocol Name P-MTAB-31099 P-MTAB-31100 P-MTAB-31101 P-MTAB-31102 P-MTAB-31104 P-MTAB-31105 Protocol Type grow extraction sequencing bioassay_data_transformation scanning nucleic acid library construction protocol Protocol Description Lymphoblast cell lines were obtained for seven primate species. All cell lines were transformed by the Epstein Barr virus except for the macaque cell lines that were transformed by a herpesvirus. Cells were grown in suspension at a confluency of 200 000-1 x106 cells/ml in RPMI1640 media supplemented with 10% Fetal Bovine Serum and 2 mM L-glutamine. C57BL/6J mice were housed in the Biological Resources Unit under UK Home Office licensing. Tissue was obtained from at least two independent males and cross-linked as described in (Schmidt, Methods,2009). Male and female human tissue samples were obtained from biopsied tissue collected at Addenbrooke's Hospital, Cambridge, and were provided by the Biobank under human tissue license 08/H0308/117. Liver tissue was also obtained from the Liver Tissue Distribution Program (NIDDK contract number N01-DK-9-2310) at the University of Pittsburgh. 1x10^8 cells were cross-linked with 1% formaldehyde as previously described (Schmidt, Methods,2009). ChIP-seq assays were performed as previously described (Schmidt, 2009). Immunoprecipitated DNA was end-repaired, A-tailed and single-end Illumina sequencing adapters ligated before 18 cycles of PCR amplification. 200-300 bp DNA fragments were selected and 36 bp reads sequenced on an Illumina Genome Analyser II according to manufacturer's instructions. ChIP and input sequencing reads from all LCL datasets were aligned using Bowtie 0.12.7 with the parameters O-n 2 -m 3 -k 1 -best to the following genome assemblies: human GRCh37, chimpanzee CHIMP2.1, gorilla gorGor3, orangutan PPYG2, macaque Mmul 1, and marmoset C. jaccus 3.2.1. Scanning was carried out according to manufacturer's specifications. Protein-bound DNA was immunoprecipitated with antibodies against CTCF (Millipore, 07-729), or YY1 (Santa Cruz, sc-281). Protocol Hardware Illumina Genome Analyzer II Comment[AdditionalFile] PEAK_CALLING.tar Comment[SecondaryAccession] ERP002246 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR231584-ERR231630 SDRF File E-MTAB-1511.sdrf.txt Publication DOI 10.1186/gb-2013-14-12-r148