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Sample GSM3720854 Query DataSets for GSM3720854
Status Public on Dec 31, 2019
Title ATAC_Mono_WT_Spleen_Toxo
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
cell type: Monocyte
infection: Toxoplasma gondii infection
genotype: Wt (CD45.1)
Extracted molecule genomic DNA
Extraction protocol 20000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations and/or insufficient mapping quality) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Reads mapping in chrM were removed with a custom script and samtools view
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal
 
Submission date Apr 12, 2019
Last update date Dec 31, 2019
Contact name Stanislas Goriely
E-mail(s) stgoriel@ulb.ac.be
Phone +3226509586
Organization name Université Libre de Bruxelles
Lab IMI
Street address Rue Adrienne Bolland 8
City Gosselies
ZIP/Postal code B-6041
Country Belgium
 
Platform ID GPL19057
Series (1)
GSE129724 Multi-step Epigenetic Programming of Monocytes during Infection
Relations
BioSample SAMN11405719
SRA SRX5674987

Supplementary file Size Download File type/resource
GSM3720854_ATAC_Mono_WT_Spleen_Toxo.bigwig 58.4 Mb (ftp)(http) BIGWIG
GSM3720854_ATAC_Mono_WT_Spleen_Toxo.narrowPeak.gz 1.1 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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