Submit ChIP-seq raw data to www.ebi.ac.uk/arrayexpress (Project E-MTAB-10475)

https://www.ebi.ac.uk/fg/annotare/login/

1. 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
   

2. 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
   

3. Publications

4. 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
   

5. 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)
   

6. 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
   

7. 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
   ...
   

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