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| Status |
Public on May 09, 2022 |
| Title |
C2C12-G-G1-replicate2 |
| Sample type |
SRA |
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| Source name |
C2C12 cell line
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| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: growing state, G1 phase
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| Treatment protocol |
C2C12 cells in the growing state were treated with trypsin and centrifuged for 5 min. The pelleted cells were resuspended and stained with 1× PBS containing Hoechst 33342 (Nacalai Tesque Inc.) for 15 min. The suspension was analyzed using a cell sorter (SONY, SH800).
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| Growth protocol |
The mouse myoblast C2C12 cell line was maintained in Dulbecco’s modified Eagle’s medium (DMEM) with 1 g/L glucose (Gibco™, Thermo Fisher Scientific) containing 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained from the C2C12 cells using Sepasol-RNA I Super G (Nacalai Tesque Inc.) and ethanol precipitation.
Sequencing was performed in an Illumina Illumina HiSeq1500 system with 101 cycles for both read 1 and read 2 using HiSeq PE Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2 (200 Cycles) for RNA-seq, and with 51 cycles for read 1 using TruSeq SBS Kit v3-HS (50 Cycles) and TruSeq SR Cluster Kit v3-cBot-HS for ChIP-seq.
C2C12 cells were sorted into three groups on the basis of the cell cycle (G1, S, and G2-M phases) and used for RNA-seq analysis. The C2C12 cells in the three groups (G1, S, and G2-M phases) were used for the ChIP-seq analysis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
kudou_mRNAseq_genes_featurecounts.txt
C2C12-G1-L2.bam
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| Data processing |
For RNA-seq, the raw sequence reads (fastq file) were mapped to the GRCm38 reference genome using HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0), and BAM files were created using SAMtools (H. Li, 2009, H. Li, 2011) (version 1.6).
Mapped reads were counted using featureCounts (Liao Y et al., 2014) (version 1.5.0) and a count matrix was created.
The downstream analysis was carried out with R (version 4.0.1).
For ChIP-seq analysis, Bowtie2 (B. Langmead et al., 2012) (version 2.3.0) was used to map the raw sequence reads (fastq) to the mouse mm10 reference genome, and BAM files were created using SAMtools.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ChIP-seq signal tracks (bigWig) were created using deepTools (Ramírez et al., 2016) (version 3.5.0). The bin size was 200 bp and window size was 10 kbp, except for H3K27me3 where the bin size was 200 bp and window size was 10 kbp.
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix.
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| Submission date |
Nov 11, 2020 |
| Last update date |
May 09, 2022 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
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| Organization name |
Medical Institute of Bioregulation
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| Lab |
Division of Transcriptomics
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| Street address |
3-1-1 Maidashi
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| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE161307 |
Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle |
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| Relations |
| BioSample |
SAMN16769224 |
| SRA |
SRX9486799 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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