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Sample GSM6598200 Query DataSets for GSM6598200
Status Public on Feb 02, 2023
Title Aged, replicate 1, scATAC-seq
Sample type SRA
 
Source name Hindlimb skeletal muscle
Organism Mus musculus
Characteristics cell type: Single nuclei
tissue: Hindlimb skeletal muscle
strain: Pax7CreER/+;Rosa26TdTomato/+
age: 28-29 months
Extracted molecule genomic DNA
Extraction protocol Young (3 months old) and aged (28-29 months old) Pax7CreER/+;Rosa26TdTomato/+ female mice were obtained from a breeding colony at UM. All mice were fed normal chow ad libitum and housed on a 12:12 hour light-dark cycle under UM veterinary staff supervision. All procedures were approved by the University Committee on the Use and Care of Animals at UM and the Institutional Animal Care and Committee and were in accordance with the U.S. National Institute of Health (NIH).
Mouse hindlimb muscles were extracted and placed into separate petri dishes containing ice-cold PBS. Using surgical scissors, muscle tissues were minced and placed into 20mL of digestion buffer (DMEM with Collagenase type II (0.2%) and Dispase II (2.5U/mL)) per mouse. Samples were placed on a shaker in a 37˚C incubator for 1.5 hours and mixed by pipette every 30 minutes. The enzymes were then inactivated by addition of 20mL 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media. The solution was passed through a 70um cell strainers, centrifuged, washed in PBS containing 3% BSA, and nuclei isolation was performed according to 10x Demonstrated Protocol CG000375 Revision B starting at step 1.1c. Nuclei from two age-matched mice were pooled prior to sorting, at step 1.1n, and 7-AAD+ nuclei were sorted on a Sony MA900 or MoFlo Astrios 3. Sorted nuclei were then permeabilized according to the same protocol.
10,000 permeabilized nuclei were loaded onto the 10x Genomics Chromium single cell controller and single nuclei were captured into nanoliter-scale gel bead-in-emulsions (GEMs). Single nuclei ATAC library constructions were performed using the ATAC-seq Next GEM kit (10x Genomics). All libraries were submitted for 51x51bp paired-end sequencing on a NovaSeq 6000 with 50,000 targeted reads per cell.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing Raw sequencing data were demultiplexed and converted to FASTQ files using the ‘bcl-convert’ command (Illumina, v3.9.3) and aligned to the mm10 reference genome (refdata-cellranger-arc-mm10-2020-A-2.0.0) using cellranger-atac count (v2.1.0).
Assembly: mm10
Supplementary files format and content: Tab-separated ATAC fragment files and corresponding tabix indexes generated by CellRanger.
 
Submission date Sep 23, 2022
Last update date Feb 02, 2023
Contact name Carlos Andres Aguilar
E-mail(s) caguilar@umich.edu
Organization name University of Michigan, Ann Arbor
Department Biomedical Engineering
Lab Aguilar Lab
Street address 2800 Plymouth Rd
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL24247
Series (2)
GSE214046 Three-dimensional chromatin re-organization during muscle stem cell aging [scATAC-seq]
GSE214047 Three-dimensional chromatin re-organization during muscle stem cell aging
Relations
BioSample SAMN30985537
SRA SRX17682715

Supplementary file Size Download File type/resource
GSM6598200_Aged_atac_fragments.tsv.gz 1.9 Gb (ftp)(http) TSV
GSM6598200_Aged_atac_fragments.tsv.gz.tbi.gz 1.0 Mb (ftp)(http) TBI
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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