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Sample GSM4002723 Query DataSets for GSM4002723
Status Public on Aug 02, 2020
Title ATAC_HC56
Sample type SRA
Source name monocytes from healthy human donnor
Organism Homo sapiens
Characteristics subject status: Healthy control
tissue: Peripheral Blood
cell type: monocyte CD14+
Growth protocol PBMCs were isolated from sodium-heparinised whole blood by Ficoll and 10-20 million PBMCs were frozen in FBS with 20% DMSO in liquid nitrogen. PBMCs were thawed and CD14hi monocytes were isolated by fluorescence-activated cells sorting (FACS) on a BD FACS Aria III
Extracted molecule genomic DNA
Extraction protocol 20000 to 50000 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 NovaSeq 6000
Description ATAC-seq in liver monocytes from healthy human donnor
Data processing Adapters were removed with Trimmomatic-0.36 with the following parameters : Nextera1.fa:1:25:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to GRCh38 by Bowtie2 with the following parameters : --X 2000 --fr --very-sensitive --no-discordant --no-mixed –non-deterministic
Reads from the alignment were sorted and indexed according to chromosome positions
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Reads mapping in chrM were removed with a custom script and samtools view
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal
Submission date Aug 02, 2019
Last update date Aug 03, 2020
Contact name Stanislas Goriely
Phone +3226509586
Organization name Université Libre de Bruxelles
Street address Rue Adrienne Bolland 8
City Gosselies
ZIP/Postal code B-6041
Country Belgium
Platform ID GPL24676
Series (2)
GSE135284 Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis [ATAC-seq]
GSE135286 Epigenetic basis for monocyte dysfunction in acute-on-chronic liver failure and alcoholic hepatitis
BioSample SAMN12430294
SRA SRX6640535

Supplementary file Size Download File type/resource
GSM4002723_ATAC_HC56.bigwig 93.0 Mb (ftp)(http) BIGWIG
GSM4002723_ATAC_HC56.narrowPeak.gz 1.7 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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