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| Status |
Public on Jan 27, 2022 |
| Title |
MUC5845_10105_24h_Ad_HEP |
| Sample type |
SRA |
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| Source name |
Hepatocyte Nuclei
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hepatocyte Nuclei
feeding state: 24h_Ad
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Approximately 25,000 bead-bound nuclei from INTACT reactions were transposed in a 50 μL volume of 1X TTBL buffer and 3.5 μL TTE Mix V50 (from TruePrep™ DNA Library Prep Kit V2 for Illumina, Vazyme TD501) for 30 minutes at 37°C. Fragmented genomic DNA was recovered using Buffer ERC coupled with MinElute spin column purification (Qiagen). Samples originating from MAC INTACT mice were run in technical duplicates.
Transposed genomic DNA was amplified by 12 cycles of quantitative PCR. Amplified DNA was purified and size-selected on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 4000 platform.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
IP'ed nuclei from HEP-INTACT mice
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| Data processing |
Sequence tags from ATAC-seq libraries were aligned to the mm10 using the BWA aligner (version 0.7.5a-r405) (Li and Durbin, 2009).
Post-alignment processing of reads was performed with Samtools (0.1.19-44428cd) (Li et al., 2009) by removing duplicate reads and filtering for high quality reads using Samtools view using the following settings ”-b -h -f 1 -F 4 -F 8 -F 256 -F 2048 -q 30”. Furthermore, only reads with a fragment length<100bp was used corresponding to the reads located in nucleosome-free regions.
ATAC seq peaks were identified, annotated and tags in peaks were counted using HOMER (Heinz et al., 2010). Tag directories from conditions with technical duplicates were combined into one before further analyses. Peaks were called in each library with HOMER findPeaks using the following settings: ‘peaks’, ‘-fragLength 70’, ‘-style factor’, ‘-minDist 140’, ‘-size 70’.
For all peak files, overlapping peaks were merged and collected in one master peak file. Tags were then counted in a 200bp window around the peak centers for each individual library in the resulting master peak file.
Differential accessible sites (fed vs fasted) were determined using DESeq2 using default parameters.
Bedgraph files for individual libraries were generated using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Bedgraph files for each condition were generated by merging the individual tag directories of one condition into one and using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with norm counts and log2FC (fed vs fasted) (output from DESeq2)
Supplementary_files_format_and_content: Bedgraph files for individual libraries
Supplementary_files_format_and_content: Bedgraph files (merged) - one from each condition
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| Submission date |
Apr 01, 2020 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Anne Loft |
| E-mail(s) |
anlo@bmb.sdu.dk
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| Organization name |
University of Southern Denmark
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| Department |
Biochemistry & Molecular Biology
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| Street address |
Campusvej 55
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| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE147922 |
Cell Type-Specific Genomic Profiling of the Hepatic Fasting Response |
| GSE147925 |
A Macrophage-Hepatocyte Glucocorticoid Receptor Axis Coordinates Fasting Ketogenesis |
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| Relations |
| BioSample |
SAMN14519463 |
| SRA |
SRX8042436 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4448933_MUC5845_10105_24h_Ad_alb_TD.ucsc.bedGraph.gz |
136.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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