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Sample GSM1406303 Query DataSets for GSM1406303
Status Public on Sep 26, 2014
Title Blueprint_S00NN3H1_H3K4me3
Sample type SRA
Source name Macrophages(BC17)
Organism Homo sapiens
Characteristics cell type: Macrophages(BC17)
Treatment protocol Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum. Monocytes were collected at different time points (0 h and 6 d after treatment) and counted before further treatment for chromatin immunoprecipitation or DNaseI treatment.
Growth protocol Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum.
Extracted molecule genomic DNA
Extraction protocol Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using HiSeq 2000 as recommended by the manufacturer. DNaseI treatment was done on isolated nuclei for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for 24hrs/25000rpm at 16ºC . Further sequenced using HiSeq as recommended by the manufacturer.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description chromatin IP
raw file: H0LRGAGXX_1_5640.sorted.bam
Data processing Cluster generation and sequencing were performed using the Illumina HiSeq2000 genome analyzer. The image files were processed to extract DNA sequence data using CASAVA-1.8.2. The 42 bp sequence tags were mapped to the reference human genome hg19 (NCBI build37), using the BWA allowing one mismatch. Only uniquely mapped-reads were used for data analysis and visualization. The output data were converted to bam files for downstream analysis. Details about aligner version and parameters used are stored in the headers of the BAM files. PCR duplicates were removed, therefore the final BAM files only contain uniquely mapped reads. Wig files were generated by counting the number of sequence reads (directionally extended to a final 300 bp) per 10-bp genomic window and can be used for viewing the data in the UCSC Genome Browser.
DNAseI bam files were merged per source-treatment (Monocytes RPMI, Macrophages RPMI, Macrophages LPS, Macrophage BG), and DNaseI hotspots were called on the merged bam using the published “Hotspots” pipeline (Neph et al 2012).
Peak calling was performed using MACS2- using Blueprint C000S5H2 Input Monocytes as a reference input.
For archiving RNA-seq 42-bp reads were aligned to hg19 using GSNAP release 2012-07-20 using parameters -N 1 -n 1 -m 1 -Q.
Gene expression quantification was performed by first aligning RNA-Seq tags to the Ensembl GRCh37 version 68 transcriptome using bowtie with parameters "-a --best --strata -S -m 100 --chunkmbs 256". Name sorted bamfiles were converted using bam2hits and gene expression was quantitated using mmseq (doi: 10.1186/gb-2011-12-2-r13). Results are given in log (base e) RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Bed.gz files are the peak regions called by MACS2, wig.gz files visualizes the mapped data in the UCSC genome browser. RNA-Seq results are reported as log (base e) RPKM.
Submission date Jun 09, 2014
Last update date May 15, 2019
Contact name Hindrik Kerstens
Organization name Radboud University
Department Molecular Biology
Lab Stunnenberg
Street address Geert Grooteplein Zuid 26
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platform ID GPL18573
Series (1)
GSE58310 Epigenetic programming during monocyte to macrophage differentiation and trained innate immunity
BioSample SAMN02843348
SRA SRX581541

Supplementary file Size Download File type/resource
GSM1406303_BG_H3K4me3_5640_NR.bed.gz 103.0 Mb (ftp)(http) BED
GSM1406303_BG_H3K4me3_5640_NR.wig.gz 9.6 Mb (ftp)(http) WIG
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Raw data are available in SRA
Processed data provided as supplementary file

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