|
| Status |
Public on Sep 10, 2019 |
| Title |
mouse liver ATAC-seq LKO4 |
| 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 |
SAMN11659751 |
| SRA |
SRX5846438 |
