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Sample GSM5600223 Query DataSets for GSM5600223
Status Public on Jan 13, 2022
Title C2C12 Am80
Sample type SRA
 
Source name C2C12 myotube
Organism Mus musculus
Characteristics cell line: C2C12
strain: C57BL/6
cell type: Myotube
treatment: Am80
Treatment protocol Microgravity conditions were produced using a 3D-Clinorotation apparatus (GraviteĀ®, Space Bio-Laboratories Co., Ltd.). This device produces an environment similar to that of outer space (0.001 G) by rotating a sample around two axes, integrating a gravity vector with a temporal axis. This is accomplished by rotation of a chamber at the center of the device, which results in uniform dispersion of the gravity vector within a spherical volume, with a constant angular velocity. Within 8 min, these conditions produced a simulated environment of 10-3 G, measured with a gravity acceleration sensor, which was defined as simulated microgravity. Differentiated C2C12 myotubes were cultured in a cell culture flask (T-75, Corning) filled with differentiation media for 8, 24, and 48 hours under simulated microgravity at 37C. As a control, C2C12 myotubes cultured in the same cell culture flask under the ground condition were used. 100 nM Am80 was added to the culture media as a compound that suppresses myotube atrophy (PNAS 118: e2102895118) to assess effects of this compound on the atrophy-associated changes in chromatin accessibility.
Growth protocol C2C12 myoblasts (ATCC CRL-1772) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin. Myogenic differentiation was induced in DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37C under 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted from approximately 50,000 cells. After transposase reactions, cellular DNA was immediately purified. The DNA was amplified for 14 cycles using Nextera primer Ad1 and a unique Ad2.n barcoding primer with NEBNext High-Fidelity 2XPCR Master Mix (NEB). The resulting libraries were size selected to 175-225 bp, purified.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 1500
 
Description Am80 treated
Data processing Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
 
Submission date Sep 28, 2021
Last update date Jan 13, 2022
Contact name Ichiro Manabe
E-mail(s) manabe-tky@umin.ac.jp
Organization name Chiba University
Street address 1-8-1 Inohana, Chuo
City Chiba
ZIP/Postal code 260-8670
Country Japan
 
Platform ID GPL18480
Series (2)
GSE184907 Analysis of accessible chromatin regions in response to microgravity in C2C12 mouse myotubes
GSE184911 Global changes of enhancer and chromatin accessibility due to microgravity in C2C12 myotubes
Relations
BioSample SAMN21880142
SRA SRX12384029

Supplementary file Size Download File type/resource
GSM5600223_C2C12_Am80.ucsc.bedGraph.gz 64.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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