|
Status |
Public on Dec 05, 2019 |
Title |
RNA-seq knockout replicate 7 [TA RNA-seq] |
Sample type |
SRA |
|
|
Source name |
Tibialis anterior muscle homogenate
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6J genotype: UBC-CreERT2;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 |
W389-Mu-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.
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|
|
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 |
SAMN12233458 |
SRA |
SRX6418163 |