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Sample GSM3932064 Query DataSets for GSM3932064
Status Public on Dec 05, 2019
Title RNA-seq wildtype replicate 4 [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 40-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 SAMN12233468
SRA SRX6418153

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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