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Sample GSM4812427 Query DataSets for GSM4812427
Status Public on Oct 02, 2020
Title PHx, 96hr_scATAC
Sample type SRA
 
Source name liver hepatocytes
Organism Mus musculus
Characteristics tissue: liver
age: 10-12 weeks old
time point: 96h
protocol: PHx surgery
Treatment protocol 10-12 weeks old mice underwent partial hepatectomy surgery
Growth protocol Mice were fed with normal diet
Extracted molecule genomic DNA
Extraction protocol Hepatocytes were isolated using two-step collagenase perfusion method
scATAC-seq libraries were prepared for sequencing according to the Chromium Single Cell ATAC Reagent Kits User Guide v1 Chemistry
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 96h post-PHx surgery
Data processing The Cell Ranger ATAC Software Suite was used for demultiplexing sequencing information
Nuclei were filtered with unique fragments greater than 1000 and TSS enrichment greater than 4
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak files contain the peak calling results for pre- and post-PHx samples, respectively.
 
Submission date Oct 01, 2020
Last update date Oct 06, 2020
Contact name Anna Mae Diehl
Organization name Duke University
Street address Research Drive
City Durham
ZIP/Postal code 27710
Country USA
 
Platform ID GPL24247
Series (2)
GSE158873 Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [scATAC-Seq]
GSE158874 Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration
Relations
BioSample SAMN16327841
SRA SRX9228268

Supplementary file Size Download File type/resource
GSM4812427_PHx_96hr_barcodes.tsv.gz 19.9 Kb (ftp)(http) TSV
GSM4812427_PHx_96hr_matrix.mtx.gz 22.1 Mb (ftp)(http) MTX
GSM4812427_PHx_96hr_peaks.bed.gz 623.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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