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Sample GSM4002733 Query DataSets for GSM4002733
Status Public on Aug 02, 2020
Title ATAC_AH31
Sample type SRA
 
Source name monocytes from human donnor with Acute on Chronic Liver Failure
Organism Homo sapiens
Characteristics subject status: Acute on Chronic Liver Failure
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 human donnor with Acute on Chronic Liver Failure
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
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 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
Relations
BioSample SAMN12430304
SRA SRX6640545

Supplementary file Size Download File type/resource
GSM4002733_ATAC_ACLF31.bigwig 106.2 Mb (ftp)(http) BIGWIG
GSM4002733_ATAC_ACLF31.narrowPeak.gz 1.4 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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