|
| Status |
Public on Jul 20, 2021 |
| Title |
tRIP-seq_CPSF6_C2C12 |
| Sample type |
SRA |
| |
|
| Source name |
Myoblast
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
treatment: no treatment
cell type: Myoblast
|
| Growth protocol |
C2C12 cells were grown in DMEM with 10% fetal bovine serum at 37°C in 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells
tRIP was performed as previously described: Masuda et al. (2020):tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly. EMBO Rep PMID: 32189459
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: tRIP-seq
For paired-end read data, only P5 reads were used for analysis.
After standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10).
Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b).
Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b).
Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with a "--binsize 1" parameter.
|
| |
|
| Submission date |
Nov 17, 2020 |
| Last update date |
Jul 20, 2021 |
| Contact name |
Akio Masuda |
| E-mail(s) |
amasuda@med.nagoya-u.ac.jp
|
| Phone |
+81-52-744-2447
|
| Organization name |
Nagoya University Graduate School of Medicine
|
| Lab |
Neurogenetics
|
| Street address |
65 tsurumai-cho, Showa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL16417 |
| Series (2) |
| GSE161602 |
Genome-wide maps of RNA-protein interactions of SRSF3, hnRNPK and CPSF6 |
| GSE161699 |
Splicing regulation of large exons secures phase-separation of transcription factors in vertebrates |
|
| Relations |
| BioSample |
SAMN16816023 |
| SRA |
SRX9620478 |
