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General Information
Title: ChIP-seq of primary human macrophages uninfected or infected with Yersinia enterocolitica strainsDescription: Pathogenic bacteria Yersinia enterocolitica injects virulence plasmid-encoded effectors through the type three secretion system into macrophages to modulate gene expression. At this point it is not known whether epigenetic modifications play a role in Yersinia regulation of gene expression. To answer this question primary human macrophages were infected with mock, WAC (virulence plasmid-cured strain) or WA314 (wild type) and samples were subjected to ChIP-seq for H3K4me3, H3K4me1, H3K27ac and H3K27me3. The effect of effector proteins YopM and YopP on histone modifications in macrophages was analyzed using a wild type strain lacking either YopM or YopP and subsequent ChIP-seq analysis.Experiment Type: 4C, antigen profiling, ATAC-seq, Bisulfite-seq, Capture-C, ChIP-chip by array, ChIP-chip by SNP array, ChIP-chip by tiling array, ChIP-seq*, CLIP-seq, comparative genomic hybridization by array, CUT&RUN, DNA-seq, exome sequencing, FAIRE-seq, genotyping by array, genotyping by high throughput sequencing, GRO-seq, Hi-C, MBD-seq, MeDIP-seq, methylation profiling by array, methylation profiling by high throughput sequencing, microRNA profiling by array, microRNA profiling by high throughput sequencing, MNase-seq, MRE-seq, proteomic profiling by array, Ribo-seq, RIP-chip by array, RIP-seq, RNA-seq of coding RNA, RNA-seq of coding RNA from single cells, RNA-seq of non coding RNA, RNA-seq of non coding RNA from single cells, RNA-seq of total RNA, scATAC-seq, single nucleus RNA sequencing, spatial transcriptomics by high-throughput sequencing, tiling path by array, transcription profiling by array, transcription profiling by RT-PCRExperimental Designs: cell type comparison design; stimulus or stress design2019-01-01
Contacts
xxx.x@uke.deInstitute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE)Martinistraße 52, 20246 Hamburg, Germanydata analystexperiment performersubmitteryyy.y@uke.deinvestigator
Publications
Create samples, add attributes and experimental variables
#Header: Name Organism CellType Stimulus MateiralType ImmunoprecipitateSample 1Homo sapiensmacrophageY. enterocolitica WA314deltaYopMDNAH3K27acSample 2Homo sapiensmacrophageY. enterocolitica WA314deltaYopMDNAH3K27acSample 3Homo sapiensmacrophageY. enterocolitica WA314deltaYopPDNAH3K27acSample 4Homo sapiensmacrophageY. enterocolitica WA314deltaYopPDNAH3K27acSample 5Homo sapiensmacrophagemockDNAH3K27acSample 6Homo sapiensmacrophagemockDNAH3K27acSample 7Homo sapiensmacrophageY. enterocolitica WACDNAH3K27acSample 8Homo sapiensmacrophageY. enterocolitica WACDNAH3K27acSample 9Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27acSample 10Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27acSample 11Homo sapiensmacrophagemockDNAH3K27me3Sample 12Homo sapiensmacrophagemockDNAH3K27me3Sample 13Homo sapiensmacrophageY. enterocolitica WACDNAH3K27me3Sample 14Homo sapiensmacrophageY. enterocolitica WACDNAH3K27me3Sample 15Homo sapiensmacrophageY. enterocolitica WACDNAH3K27me3Sample 16Homo sapiensmacrophageY. enterocolitica WACDNAH3K27me3Sample 17Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27me3Sample 18Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27me3Sample 19Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27me3Sample 20Homo sapiensmacrophageY. enterocolitica WA314DNAH3K27me3Sample 21Homo sapiensmacrophagemockDNAH3K4me1Sample 22Homo sapiensmacrophagemockDNAH3K4me1Sample 23Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me1Sample 24Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me1Sample 25Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me1Sample 26Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me1Sample 27Homo sapiensmacrophagemockDNAH3K4me3Sample 28Homo sapiensmacrophagemockDNAH3K4me3Sample 29Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 30Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 31Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 32Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 33Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3Sample 34Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3Sample 35Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3Sample 36Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3Sample 37Homo sapiensmacrophageY. enterocolitica WA314deltaYopMDNAH3K4me3Sample 38Homo sapiensmacrophageY. enterocolitica WA314deltaYopMDNAH3K4me3Sample 39Homo sapiensmacrophageY. enterocolitica WA314deltaYopPDNAH3K4me3Sample 40Homo sapiensmacrophageY. enterocolitica WA314deltaYopPDNAH3K4me3Sample 41Homo sapiensmacrophagemockDNAH3K4me3Sample 42Homo sapiensmacrophagemockDNAH3K4me3Sample 43Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 44Homo sapiensmacrophageY. enterocolitica WACDNAH3K4me3Sample 45Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3Sample 46Homo sapiensmacrophageY. enterocolitica WA314DNAH3K4me3
Assign ENA library information
#Header: NameResize Library Layout * Library Source * Library Strategy * Library Selection * Library Strand Nominal Length Nominal SDev OrientationSample 1SINGLEGENOMIC (Genomic DNA (includes PCR products from genomic DNA))ChIP-Seq (Direct sequencing of chromatin immunoprecipitates)ChIP (Chromatin immunoprecipitation)Sample 2SINGLEGENOMIC (Genomic DNA (includes PCR products from genomic DNA))ChIP-Seq (Direct sequencing of chromatin immunoprecipitates)ChIP (Chromatin immunoprecipitation)
Describe protocols
#Header: Name Assign protocols to samples Type Description * Performer ** Hardware ** SoftwareProtocol 1Assign...Type: sample collection protocolDescription: Human peripheral blood monocytes were isolated by centrifugation of heparinized blood in Ficoll. Monocytic cells were isolated with magnetic anti-CD14 antibody beads and an MS+ Separation Column (Miltenyi Biotec) according to the manufacturer’s instructions and seeded into 6-well plates at a density of 2 × 106 cells. Cells were cultured in RPMI containing 20% autologous serum at 37°C, 5% CO2, and 90% humidity. The medium was changed every three days until cells were differentiated into macrophages after 7 days. Macrophages were used for infection 1-2 weeks after the isolationProtocol 2Assign...nucleic acid extraction protocolFor the ChIP with formaldehyde crosslinking, macrophages (~3-10 x 106 cells per condition) were washed once with warm PBS and incubated for 30 min at 37 °C with accutase (eBioscience, USA) to detach the cells. ChIP protocol steps were performed as described in (Günther et al., 2016, PMID: 26855283), except that BSA-blocked ChIP grade protein A/G magnetic beads (Thermo Fisher Scientific, USA) were added to the chromatin and antibody mixture and incubated for 2 h at 4 °C rotating to bind chromatin-antibody complexes. Samples were incubated for ~3 min with a magnetic stand to ensure attachment of beads to the magnet and mixed by pipetting during the wash steps.Protocol 3Assign...nucleic acid library construction protocolChIP-seq libraries were constructed with 1-10 ng of ChIP DNA or input control asa starting material. Libraries were generated using the NEXTflex™ ChIP-Seq Kit(Bioo Scientific, USA) as per manufacturer’s recommendations. Concentrations of allsamples were measured with a Qubit Fluorometer (Thermo Fisher Scientific, USA)and fragment length distribution of the final libraries was analysed with the DNAHigh Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).Protocol 4Assign...nucleic acid sequencing protocolAll samples were normalized to 2 nM and pooled equimolar. The library pool was sequenced on the NextSeq500 (Illumina, USA) with 1 x 75 bp and total at least ~18 million reads per sample.Technology Platform Next Generation Sequencing Heinrich Pette Institute, Leibniz Institute for Experimental Virology Martinistraße 52 20251 HamburgNextSeq 500
Assign data files
#Header: NameResize Raw Data FileSample 1H3K27ac_dM_DoA.fastq.gzSample 2H3K27ac_dM_DoB.fastq.gzSample 3H3K27ac_dP_DoA.fastq.gzSample 4H3K27ac_dP_DoB.fastq.gzSample 5H3K27ac_mock_DoA.fastq.gz...
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