|
| Status |
Public on Dec 05, 2019 |
| Title |
RNA-seq wildtype replicate 5 [TA RNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Tibialis anterior muscle homogenate
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: WT;Hic1F/F
tissue: Whole TA muscle
|
| Treatment protocol |
Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before a 1 year experimental period before harvest of TA muscles.
|
| Growth protocol |
Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole TA muscles were homogenized in RNAzol lysis reagent and further processed as per manufacturer's instructions to obtain RNA for library preparation and subsequent NGS.
TruSeq stranded mRNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
W384-Mu-2-R
processed data file: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx
|
| Data processing |
Basecalls were made using RTA v2.1.
Demultiplexing was achieved using bcl2fastq2.
Alignment was performed using Tophat 2 with Bowtie 2.
FPKM values were generated using Cufflinks.
Ingenuity Pathway Analysis was run using a differential expression list generated by Cufflinks filtered for p < 0.05.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Supplemental_Table_3_RNA-seq_18m_Hic1_cKO_whole_TA_muscle_gene_expression.xlsx: Excel file includes FPKM values for each sample.
|
| |
|
| Submission date |
Jul 08, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Tully Michael Underhill |
| E-mail(s) |
tunderhi@brc.ubc.ca
|
| Phone |
604-822-5833
|
| Organization name |
University of British Columbia
|
| Department |
Biomedical Research Centre
|
| Street address |
2222 Health Sciences Mall
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 1Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE110038 |
Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration |
| GSE133995 |
RNA-seq profiling of adult skeletal muscle after long term conditional knockout of Hic1 [TA RNA-seq] |
|
| Relations |
| BioSample |
SAMN12233467 |
| SRA |
SRX6418154 |
