|
| Status |
Public on Aug 04, 2020 |
| Title |
F1-1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA from a single EDL myofiber
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: a single EDL myofiber
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Single myofiber RNA was extracted by adding 1 ul of 10X lysis buffer and 9 ul of RNAse free water in 0.2 ml micro tubes using DNA SMART-Seq HT kit available from Takara Biosciences; whole muscle RNA was extracted using Trizol method.
Libraries were prepared using DNA SMART-Seq HT kit from Takara Biosciences following manufacturer’s recommendation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq files were mapped using hisat2 using a index that comes the GRCm38/mm10 genome and ENSEMBL transcriptome (“grcm38_tran” downloaded from the hisat2 website); mapping used default parameters; this resulted in sam files
sam files were converted to bam, sorted and indexed using samtools
Indexed bam files were counted using featureCounts and ENSEMBL gene definitions (“Mus_musculus.GRCm38.97.gtf” obtained from ENSEMBL website), producing ReadCounts.csv
Genome_build: GRCm38/mm110
Supplementary_files_format_and_content: ReadCounts.csv has gene ids on rows, the twelve samples on columns, and reports read counts in a comma-separated text file
|
| |
|
| Submission date |
Aug 04, 2019 |
| Last update date |
Aug 04, 2020 |
| Contact name |
Theodore Perkins |
| E-mail(s) |
theodore.j.perkins@gmail.com
|
| Phone |
6137378899
|
| Organization name |
Ottawa Hospital Research Institute
|
| Department |
Regenerative Medicine Program
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
Ontario |
| ZIP/Postal code |
K1H8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE135364 |
High Resolution Genome Wide Expression Analysis of Single Myofibers Using SMART-Seq |
|
| Relations |
| BioSample |
SAMN12495691 |
| SRA |
SRX6656651 |
