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| Status |
Public on Jul 31, 2024 |
| Title |
G_Dele1neg_Rep5 |
| Sample type |
SRA |
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| Source name |
Gastrocnemius muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: Gastrocnemius muscle
genotype: Chchd10+/+; Dele1-/-
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
G_Analysis_Results_20240604_ancova_adjusted_expression.csv
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| 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
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| Submission date |
Jul 29, 2024 |
| Last update date |
Jul 31, 2024 |
| Contact name |
Derek Paul Narendra |
| Organization name |
NINDS, NIH
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| Street address |
35 CONVENT DR, Rm. 2A-211
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| City |
BETHESDA |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE273310 |
DELE1 mitochondrial integrated stress response to CHCHD10 G58R protein misfolding in striated muscle [RNA-seq] |
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| Relations |
| BioSample |
SAMN42888644 |
| SRA |
SRX25497833 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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