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Status |
Public on Jun 18, 2020 |
Title |
Femoral homogenate - DO mouse 30 |
Sample type |
SRA |
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Source name |
Femur
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Organism |
Mus musculus |
Characteristics |
tissue: Marrow-depleted left femur - homogenate strain: Diversity Outbred (J:DO) age: 90 days
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Treatment protocol |
Ends of femurs were cut, and marrow was flushed out.
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Extracted molecule |
total RNA |
Extraction protocol |
Femurs were homogenated in TRIzol, and total RNA was extracted from homogenates using mirVana miRNA isolation kit (Life Technologies, Carlsbad, CA). Libraries were prepared using the Illumina TruSeq Stranded Total RNA HT sample prep kits
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
DO-30
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Data processing |
Basecalls were performed using the Real-Time Analysis (RTA) software version 2.4.11 Each sample/run combination was aligned to GRCm38 using HISAT2 version 2.0.5, using the GRCm38_snp index. HISAT2 was run with the following parameters: --dta --trim3 1 Aligned files were sorted, merged by sample for all runs, and sorted again using samtools version 1.10 Assembly and quantification was performed with StringTie version 1.3.3, using the GRCm38.98 GTF annotation. The following StringTie parameters were used: -e -G A single GTF was generated with all common transcripts, using StringTie --merge -G. Assembly and quantification were repeated as before, but using the merged GTF, with the -eB -G parameters. A gene count matrix was generated using the prepDE.py script, sourced from the StringTie website (http://0-ccb-jhu-edu.brum.beds.ac.uk/software/stringtie/index.shtml?t=manual) Gene counts were filtered to include genes that had more than 0.1 TPM and more than 6 reads in more than 38 samples (20%). Gene read counts were transformed using the variance stabilizing transformation (VST) from the DESeq2 package (version 1.20.0). This was followed by a quantile- based inverse Normal transformation , as performed in Yang et al., Nature, 2012. Genome_build: GRCm38 Supplementary_files_format_and_content: CSV file containing filtered gene read counts for all 192 samples Supplementary_files_format_and_content: CSV file containing transformed filtered gene read counts
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Submission date |
Jun 17, 2020 |
Last update date |
Jun 19, 2020 |
Contact name |
Basel Al-Barghouthi |
E-mail(s) |
bma8ne@virginia.edu
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Organization name |
University of Virginia
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Lab |
Farber Lab
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Street address |
P.O. BOX 800717
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City |
Charlottesville |
State/province |
VA |
ZIP/Postal code |
22908 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE152708 |
Systems genetic analysis in Diversity Outbred mice informs human bone mineral density GWAS and identifies Qsox1 as a novel determinant of bone strength |
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Relations |
BioSample |
SAMN15300785 |
SRA |
SRX8570490 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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