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| Status |
Public on Jan 13, 2022 |
| Title |
C2C12 Clino |
| Sample type |
SRA |
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| Source name |
C2C12 myotube
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| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
strain: C57BL/6
cell type: Myotube
treatment: Clinorotation
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| Treatment protocol |
Microgravity conditions were produced using a 3D-Clinorotation apparatus (Gravite®, 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.
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| 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.
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Clinorotation
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| 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.
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| Submission date |
Sep 28, 2021 |
| Last update date |
Jan 13, 2022 |
| Contact name |
Ichiro Manabe |
| E-mail(s) |
[email protected]
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| Organization name |
Chiba University
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| Street address |
1-8-1 Inohana, Chuo
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN21880140 |
| SRA |
SRX12384027 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5600221_C2C12_Clino.ucsc.bedGraph.gz |
31.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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