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Sample GSM4624275 Query DataSets for GSM4624275
Status Public on Jun 18, 2020
Title Femoral homogenate - DO mouse 80
Sample type SRA
 
Source name Femur
Organism Mus musculus
Characteristics tissue: Marrow-depleted left femur - homogenate
strain: Diversity Outbred (J:DO)
age: 77 days
Treatment protocol Ends of femurs were cut, and marrow was flushed out.
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description DO-80
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
 
Submission date Jun 17, 2020
Last update date Jun 19, 2020
Contact name Basel Al-Barghouthi
E-mail(s) bma8ne@virginia.edu
Organization name University of Virginia
Lab Farber Lab
Street address P.O. BOX 800717
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
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
Relations
BioSample SAMN15300816
SRA SRX8570605

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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