NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2516122 Query DataSets for GSM2516122
Status Public on Sep 06, 2017
Title WT3
Sample type SRA
 
Source name hindlimb muscle
Organism Mus musculus
Characteristics tissue: skeletal muscle
age: P0
genotype: WT
Extracted molecule total RNA
Extraction protocol P0 mice were sacrificed, deskinned, and hindlimb muscle was removed from the leg and flash frozen. Total RNA was extracted using QIAGEN Rneasy mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description WT-Replicate-3
Data processing Quality assessment of the RNA-Seq data was done using NGS-QC-Toolkit (Patel and Jain, 2012) with default setting
Quality filtered reads generated by the tool were then aligned to the mouse reference genome GRCm38 (mm10) using the Tophat2 (v 2.0.0 ) aligner (Kim et al., 2013) using default setting.
Differential gene expression analysis was done using the R package DESeq2 (v 1.6.3) (Anders and Huber, 2010).
Read counts were normalized by taking the median of each gene count across samples and dividing each sample gene count by the relative ratio of library sizes between the calculated median and sample size. The averaged normalized expressions values of the samples were used to calculate fold change and p-values.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CPM value for all genes calculated using edgeR
Supplementary_files_format_and_content: edgeR output in .txt format containing log2foldchange, log2CPM and LR values and p values. Data present reflect change in averaged KO samples (KO1, KO2, KO3) with respect to WT (WT1,WT2,WT3) samples. Fdr = 0.01, p-value = 0.05 were used as cut-offs.
 
Submission date Mar 01, 2017
Last update date May 15, 2019
Contact name Andres Ramirez-Martinez
E-mail(s) andres.ramirezmartinez@utsouthwestern.edu
Organization name UTSW Medical Center
Department Molecular Biology
Lab Olson Lab
Street address 6000 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390-9148
Country USA
 
Platform ID GPL17021
Series (1)
GSE95543 KLHL41 stabilizes skeletal muscle sarcomeres by nonproteolytic ubiquitination
Relations
BioSample SAMN06469837
SRA SRX2600470

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap