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Sample GSM3770626 Query DataSets for GSM3770626
Status Public on Sep 10, 2019
Title mouse liver ATAC-seq LKO1
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: liver
phenotype: HFD LKO
Extracted molecule genomic DNA
Extraction protocol Nuclei from frozen mouse liver were isolated by gradient centrifugation. 50000 isolated nuclei were used in each transposase reaction (Illumina). The sequencing libraries were barcoded and amplified by 2-step PCR. DNA sequencing were performed on Illumina NovaSeq 6000 instrument with 50-bp paired-end reads.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing FastQC was used to assess the sequencing quality on fastq files.
atactk (0.1.5) was used for adapator trimming.
bwa (0.7.17-r1188) was used for alignment to generate bam files for ATAC-seq. STAR was used for alignment to generate bam files for RNA-seq.
Duplicates were marked by Picard (v.2.8.14) for ATAC-seq.
Samtools was used to remove duplicates for ATAC-seq.
macs2 (2.1.1.20160309) was used for peak calling at FDR < 0.1 for ATAC-seq.
The treat_pileup.bedgraph files (generated by macs2) from each individual samples were normalized to its own library size and converted to bigwig file by bedGraphToBigWig (v.4).
Broad peaks were filtered against an mm10 blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz).
The master peaks list was generated from the union of all blacklist-filtered broad peaks
Bedtools (v.2.27.1) was used to count reads in each peak for each ATAC-seq sample. HTSeq was used to count reads in gene feature for each RNA-seq sample
HOMER were used to annotate peaks to closest gene for ATAC-seq.
The R package DESeq2 (v.1.20.0) was used to perform the differential peak/gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from RNA-seq, DESeq2-normalized read counts from ATAC-seq, bigwig file of ATAC-seq coverage.
 
Submission date May 16, 2019
Last update date Sep 10, 2019
Contact name Jiandie Lin
E-mail(s) jdlin@umich.edu
Phone 7346153512
Organization name University of Michigan
Department Cell & Developmental Biology, Life Science Institute
Lab Jiandie Lin Lab
Street address 210 Washtenaw Ave
City Ann Arbor
State/province MI
ZIP/Postal code 48103
Country USA
 
Platform ID GPL24247
Series (1)
GSE131336 Chromatin architecture as a checkpoint for NASH-associated liver injury
Relations
BioSample SAMN11659666
SRA SRX5846435

Supplementary file Size Download File type/resource
GSM3770626_LKO2.broad.peaks.bw 451.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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