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| Status |
Public on Jun 01, 2015 |
| Title |
DC_MTB_H3K4me1_rep2 (ChIP-Seq) |
| Sample type |
SRA |
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| Source name |
Monocyte-derived dendritic cells
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| Organism |
Homo sapiens |
| Characteristics |
condition: MTB-infected
chip anitbody: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1)
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| Treatment protocol |
Dendritic cells (DCs) were infected with a Mycobacterium tuberculosis (MTB) strain expressing green-fluorescent protein (H37Rv) for 18 h at a multiplicity of infection of 1-to-1. Full details can be found in Barreiro et al. (2012).
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| Growth protocol |
Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats by Ficoll-Paque centrifugation. Blood monocytes were then purified from PBMCs by positive selection with magnetic CD14 MicroBeads (Miltenyi Biotech). Pure monocytes were cultured for 5 days in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FCS (Dutscher), L-glutamine (Invitrogen), GM-CSF (20 ng/mL; Immunotools), and IL-4 (20 ng/mL; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned. Before infection, we systematically checked the differentiation/activation status of the monocyte-derived DCs by flow cytometry, using antibodies against CD1a, CD14, CD83, and HLA-DR. Only samples presenting the expected phenotype for non-activated DCs – CD1a+, CD14-, CD83-, and HLA-DRlow – were used in downstream experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from infected and non-infected DCs was extracted using the PureGene DNA extraction kit (Gentra Systems).
Samples from infected and non-infected DCs from two individuals were crosslinked with 1% w/v formaldehyde for 10 min at RT and immediately quenched for 5 min with 125mM Glycine at RT. The formaldehyde fixed samples were then sonicated to 100-400 bp using a Bioruptor (Diagenode) and then ChIP-DNA prepared using the IP-Star Compact (Diagenode) Indirect method with an Antibody-Antigen incubation of 10 hr, Bead incubation of 2 hr, and 4x 20 min wash steps. Approximately 1 million cells were used for each ChIP and ~50,000 cells for the input. The following antibodies were used: H3K4me1 (Company: CST, Cat. No.: 5326P, Lot No.: 1), H3K4me3 (CST, 9751BC, 7), H3K9me3 (MABI, 0318, 13001), H3K27me3 (MABI, 0323, 13001), H3K27ac (Abcam, Ab4729, GR119051), and H3K36me3 (MABI, 0333, 12003). ChIP and Input libraries were prepared using the Illumina Truseq Nano DNA kit, with alterations including: PCR enrichment (14 cycles) prior to size selection and utilizing the PippinPrep method (SAGE Science) instead of the SPRI method for size selection (200-400 bp).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Adapter sequences and low quality score bases (Phred score < 20) were first removed from reads.
Trimmed reads were mapped in bisulfite mode to human reference genome (GRCh37/hg19) and control sequences and PCR duplicates were removed.
genome build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using bedGraphToBigWig (UCSC); Scores represent the number of reads that mapped within a genomic region.
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| Submission date |
Dec 15, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alain Pacis |
| E-mail(s) |
alain.pacis@mcgill.ca
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| Organization name |
Canadian Centre for Computational Genomics (C3G)
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| Street address |
740 Dr Penfield Ave
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| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0G1 |
| Country |
Canada |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE64175 |
Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells (ChIP-Seq) |
| GSE64183 |
Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells |
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| Relations |
| BioSample |
SAMN03268980 |
| SRA |
SRX818196 |
| Named Annotation |
GSM1565804_DC178_MTB_H3K4me1.bw |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1565804_DC178_MTB_H3K4me1.bw |
151.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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