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Sample GSM5558275 Query DataSets for GSM5558275
Status Public on Nov 10, 2021
Title Treated human monocytes, rep 3
Sample type SRA
 
Source name Human monocytes
Organism Homo sapiens
Characteristics cell type: Human monocytes
treatment: MV130
Treatment protocol 1.5E+6 human monocytes were plated in in 10 cm Petri dishes and stimulated at day 0 with MV130 (3.0E+6 bacteria/plate) or excipient. After 24 hours cells were washed and left resting for 5 days.
Growth protocol Buffy coats from healthy volunteers were obtained from Andalusian Biobank. Human peripheral blood mononuclear cells (hPBMCs) were isolated by differential centrifugation using Biocoll Separating Solution and human monocytes were selected by adhesion.
Extracted molecule genomic DNA
Extraction protocol At day 5, human monocytes were detached and 50.000 cells were colleceted in ice-cold Flow cytometry buffer and immediately processed following a previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and mantained by incubation for 30 minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were generated following Buenrostro et al (2013), purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model NextSeq 2000
 
Data processing Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against HG38 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Genome_build: HG38
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.
 
Submission date Sep 05, 2021
Last update date Nov 10, 2021
Contact name Manuel J Gomez
E-mail(s) mjgomezr@cnic.es
Organization name CNIC
Lab Bioinformatics Unit
Street address Melchor Fernández Almagro, 3
City Madrid
State/province Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL30173
Series (2)
GSE183485 ATAC-Seq based chromatin accessibilty profile of human monocytes treated with MV130 or its excipient
GSE183721 Trained immunity induction by the inactivated mucosal vaccine MV130 protects against experimental viral respiratory infections
Relations
BioSample SAMN21239480
SRA SRX12020761

Supplementary file Size Download File type/resource
GSM5558275_6_MV130C_PBrandi_ATACSeq_S10.hg38_peaks.narrowPeak.gz 678.5 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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