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| Status |
Public on Nov 15, 2023 |
| Title |
cm-A-12-2 |
| Sample type |
SRA |
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| Source name |
Primary neonatal mouse cardiomyocytes
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| Organism |
Mus musculus |
| Characteristics |
cell type: Primary neonatal mouse cardiomyocytes
treatment: Ad-NAT10-12h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Pulse labeling: Seed cells the day before the labelling experiment in a density that allows exponential growth for the duration of the experiment.Pulse/chase labeling: After pulse labeling, remove s4U -containing media from the cells. IAA treatment (Protect samples from light) .
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
Slam-seq:The flow ofslamdunkis to first map your reads, filter your alignments, call variants on your final alignments and use these to calculate conversion rates, counts and various statistics for your 3’UTRs.
Slam-seq:SLAM-DUNK was used to map reads, filter alignments, call variants on final alignments and use these to calculate conversion rates, counts and various statistics for 3’UTRs.Extract and summarize the count results of tcount files into a count table.
Slam-seq:Differential gene expression analysis was performed using the DESeq2 R-package.
Slam-seq:GO and KEGG analysis were performed using clusterProfiler R package (v3.6.0).
Assembly: mm10
Supplementary files format and content: TcReadfpkm.xls
Library strategy: Slam-seq
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| Submission date |
Nov 12, 2023 |
| Last update date |
Nov 15, 2023 |
| Contact name |
Chuanxi Yang |
| E-mail(s) |
2205515@tongji.edu.cn
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| Organization name |
School of Medicine, Southeast University
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| Department |
Department of Cardiology
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| Street address |
300 Guangzhou Road, 210029, Nanjing, PR China
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| City |
Nanjing |
| State/province |
China |
| ZIP/Postal code |
211300 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE233736 |
Nat10 is involved in myocardial remodeling through ac4C-mediated transcriptomic regulation |
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| Relations |
| BioSample |
SAMN38219957 |
| SRA |
SRX22495903 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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