|
| Status |
Public on Nov 22, 2021 |
| Title |
mWT |
| Sample type |
SRA |
| |
|
| Source name |
mESCs-CM
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Ainv15
genotype: wild type
cell type: mESCs-CM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a RNeasy Mini Kit (Qiagen, 74106). RNA quality and quantifications were inspected using an Agilent 2100 Bioanalyzer.
The mRNA sequencing libraries were prepared using a Truseq Stranded mRNA kit (Illumina), and 2x150 bp paired-read sequencing was performed using an Illumina HiSeq instrument
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
On-instrument base-calling with Illumina HiSeq 2500 BclToFastq v2.18.
Adaptor sequences were removed from raw sequences, and the quality of reads was examined by FastQC software. Low-quality regions were trimmed (Phred quality score of <20).
Using STAR to map sequenced reads to whole genome, with additional parameters: --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 6 --alignIntronMax 300000
Splicing event classification was performed using rMATS v4.0.2
Gene expression level of read counts and TPM were calculated using CLC Genomics Workbench 21.
Genome_build: GRCh38/hg38, GRCm39/mm39
Supplementary_files_format_and_content: Excel xlsx files of rMATs alternative splicing results
Supplementary_files_format_and_content: tab-delimited text files include read counts and TPM for each Sample
|
| |
|
| Submission date |
Oct 25, 2021 |
| Last update date |
Nov 22, 2021 |
| Contact name |
Paul Wei-Che Hsu |
| E-mail(s) |
paul@nhri.edu.tw
|
| Phone |
+886-37-206-166
|
| Organization name |
National Health Research Institutes
|
| Department |
National Health Research Institutes
|
| Lab |
R2-3023
|
| Street address |
Zhunan: 35, Keyan Road, Zhunan Town
|
| City |
Miaoli County |
| State/province |
Taiwan |
| ZIP/Postal code |
350 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE186518 |
Alternative Splicing Mediated by RNA-binding Protein RBM24 Facilitates Cardiac Myofibrillogenesis in a Differentiation Stage-Specific Manner |
|
| Relations |
| BioSample |
SAMN22560948 |
| SRA |
SRX12764147 |
