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General Information
Title: ChIP-seq of primary human macrophages uninfected or infected with Yersinia enterocolitica strains Description: 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-PCR Experimental Designs: cell type comparison design; stimulus or stress design 2019-01-01 -
Contacts
xx x.x@uke.de Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE) Martinistraße 52, 20246 Hamburg, Germany data analyst experiment performer submitter yy y.y@uke.de investigator -
Publications
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Create samples, add attributes and experimental variables
#Header: Name Organism CellType Stimulus MateiralType Immunoprecipitate Sample 1 Homo sapiens macrophage Y. enterocolitica WA314deltaYopM DNA H3K27ac Sample 2 Homo sapiens macrophage Y. enterocolitica WA314deltaYopM DNA H3K27ac Sample 3 Homo sapiens macrophage Y. enterocolitica WA314deltaYopP DNA H3K27ac Sample 4 Homo sapiens macrophage Y. enterocolitica WA314deltaYopP DNA H3K27ac Sample 5 Homo sapiens macrophage mock DNA H3K27ac Sample 6 Homo sapiens macrophage mock DNA H3K27ac Sample 7 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27ac Sample 8 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27ac Sample 9 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27ac Sample 10 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27ac Sample 11 Homo sapiens macrophage mock DNA H3K27me3 Sample 12 Homo sapiens macrophage mock DNA H3K27me3 Sample 13 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27me3 Sample 14 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27me3 Sample 15 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27me3 Sample 16 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K27me3 Sample 17 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27me3 Sample 18 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27me3 Sample 19 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27me3 Sample 20 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K27me3 Sample 21 Homo sapiens macrophage mock DNA H3K4me1 Sample 22 Homo sapiens macrophage mock DNA H3K4me1 Sample 23 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me1 Sample 24 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me1 Sample 25 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me1 Sample 26 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me1 Sample 27 Homo sapiens macrophage mock DNA H3K4me3 Sample 28 Homo sapiens macrophage mock DNA H3K4me3 Sample 29 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 30 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 31 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 32 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 33 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 Sample 34 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 Sample 35 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 Sample 36 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 Sample 37 Homo sapiens macrophage Y. enterocolitica WA314deltaYopM DNA H3K4me3 Sample 38 Homo sapiens macrophage Y. enterocolitica WA314deltaYopM DNA H3K4me3 Sample 39 Homo sapiens macrophage Y. enterocolitica WA314deltaYopP DNA H3K4me3 Sample 40 Homo sapiens macrophage Y. enterocolitica WA314deltaYopP DNA H3K4me3 Sample 41 Homo sapiens macrophage mock DNA H3K4me3 Sample 42 Homo sapiens macrophage mock DNA H3K4me3 Sample 43 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 44 Homo sapiens macrophage Y. enterocolitica WAC DNA H3K4me3 Sample 45 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 Sample 46 Homo sapiens macrophage Y. enterocolitica WA314 DNA H3K4me3 -
Assign ENA library information
#Header: NameResize Library Layout * Library Source * Library Strategy * Library Selection * Library Strand Nominal Length Nominal SDev Orientation Sample 1 SINGLE GENOMIC (Genomic DNA (includes PCR products from genomic DNA)) ChIP-Seq (Direct sequencing of chromatin immunoprecipitates) ChIP (Chromatin immunoprecipitation) Sample 2 SINGLE GENOMIC (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 ** Software Protocol 1 Assign... Type: sample collection protocol Description: 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 isolation Protocol 2 Assign... nucleic acid extraction protocol For 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 3 Assign... nucleic acid library construction protocol ChIP-seq libraries were constructed with 1-10 ng of ChIP DNA or input control as a starting material. Libraries were generated using the NEXTflex™ ChIP-Seq Kit (Bioo Scientific, USA) as per manufacturer’s recommendations. Concentrations of all samples were measured with a Qubit Fluorometer (Thermo Fisher Scientific, USA) and fragment length distribution of the final libraries was analysed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Protocol 4 Assign... nucleic acid sequencing protocol All 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 Hamburg NextSeq 500 -
Assign data files
#Header: NameResize Raw Data File Sample 1 H3K27ac_dM_DoA.fastq.gz Sample 2 H3K27ac_dM_DoB.fastq.gz Sample 3 H3K27ac_dP_DoA.fastq.gz Sample 4 H3K27ac_dP_DoB.fastq.gz Sample 5 H3K27ac_mock_DoA.fastq.gz ...
Submit ChIP-seq raw data to www.ebi.ac.uk/arrayexpress (Project E-MTAB-10475)
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