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Sample GSM8425975 Query DataSets for GSM8425975
Status Public on Jul 31, 2024
Title G_Dele1neg_Rep3
Sample type SRA
 
Source name Gastrocnemius muscle
Organism Mus musculus
Characteristics tissue: Gastrocnemius muscle
genotype: Chchd10+/+; Dele1-/-
Extracted molecule total RNA
Extraction protocol RNA was extracted using the using the Direct-zol RNA Miniprep Kit (Zymo, catalog R2051)
RNA libraries for RNA sequencing were prepped with the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads using the manufacturer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description G_Analysis_Results_20240604_ancova_adjusted_expression.csv
Data processing In R, counts per gene were normalized by gene length first, followed by normalization for differences in sequencing depth, using the counts per million procedure. Normalized values were pedestalled by (+2) then Log2 transformed. Cross-sample normalization was then performed to correct for differences in expression of distribution spread and location, using the “cyclicloess” procedure. After inspection of results in boxplots, noise was modeled to identify and remove noise-biased genes. Values for each gene were subset per cohort and fit via lowess to produce trend lines for each experiment group, in order to determine the dynamic range. Noise-cutoffs were defined where the trends deviated from linearity. Expression values less than cut-off were floored to the cut-off and genes not having at least one sample greater than the cut-off were removed as noise-biased and non-informative. A similar procedure was used for those genes with expression with values higher than the ceiling cut-off. ~12,870 genes remained after noise floor and filter processing. ANOVA (Expression ~ Group + Sex) was applied to these followed by posthoc testing.
Assembly: GRCh38/hg38
Supplementary files format and content: comma separated values file (.csv), ANCOVA adjusted (for biological sex) expression
 
Submission date Jul 29, 2024
Last update date Jul 31, 2024
Contact name Derek Paul Narendra
Organization name NINDS, NIH
Street address 35 CONVENT DR, Rm. 2A-211
City BETHESDA
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL13112
Series (1)
GSE273310 DELE1 mitochondrial integrated stress response to CHCHD10 G58R protein misfolding in striated muscle [RNA-seq]
Relations
BioSample SAMN42888646
SRA SRX25497831

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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