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Sample GSM5140578 Query DataSets for GSM5140578
Status Public on Jun 20, 2022
Title Time-series-3min_lot2
Sample type SRA
Source name C2C12 cell line
Organism Mus musculus
Characteristics cell line: C2C12
cell type: myoblast
Treatment protocol For time series analysis, cells were washed twice with PBS and treated with 200 µL of 0.25% trypsin for 30 sec, 3 min or 30 min at 37ºC.
For low trypsin level treatment, cells were washed twice with PBS, and treated with 200 µL of 0.25% trypsin. Trypsin was removed immediately and cells were incubated at 37 °C for 3 min.
For cold-active protease treatment, cells were washed twice with PBS followed by adding 200 µL of cold protease. Cells were incubated at 4 °C for 5 min with shaking.
Growth protocol C2C12 cells were cultured in 6 well plates in Dulbecco’s modified Eagle’s medium (DMEM) (1g/L D-glucose) supplemented with 20% fetal bovine serum (FBS), 2 mM L-glutamine, and 1% penicillin-streptomycin.
Extracted molecule total RNA
Extraction protocol All samples were collected by adding lysis buffer to the cell culture plates followed by scraping (Control) and re-suspending cells. Total RNAs were extracted from lysate using NucleoSpin RNA XS (Takara).
Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2 (50 Cycles) on Illumina HiSeq 1500 sequencers, with 15 cycles for read 1 and 45 cycles for read 2.
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 1500
Data processing Library strategy: BRB-seq
Extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout.
The reads were trimmed using Cutadapt (M. Martin, 2011) (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option: -a GATCGTCGGACT. The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1). UMIs were not used and mitochondrial genes are excluded in the following analysis.
Downstream analysis was conducted by DESeq2 software (M. I. Love et al., 2014) (1.28.1).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.csv file include comma-delimited RNA-seq read count matrix, normalized count matrix, and TPM matrix.
Submission date Mar 08, 2021
Last update date Jun 20, 2022
Contact name Yasuyuki Ohkawa
Organization name Medical Institute of Bioregulation
Lab Division of Transcriptomics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 8128582
Country Japan
Platform ID GPL18480
Series (1)
GSE168452 Enzymatic treatment using trypsin and cold-active protease for C2C12 myoblasts
BioSample SAMN18205516
SRA SRX10268442

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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