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| Status |
Public on Sep 06, 2017 |
| Title |
KO3 |
| Sample type |
SRA |
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| Source name |
hindlimb muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: skeletal muscle
age: P0
genotype: Klhl41-KO
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
KO-Replicate-3
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| 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.
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| Submission date |
Mar 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andres Ramirez-Martinez |
| E-mail(s) |
andres.ramirezmartinez@utsouthwestern.edu
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| Organization name |
UTSW Medical Center
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| Department |
Molecular Biology
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| Lab |
Olson Lab
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| Street address |
6000 Harry Hines Blvd.
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9148 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE95543 |
KLHL41 stabilizes skeletal muscle sarcomeres by nonproteolytic ubiquitination |
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| Relations |
| BioSample |
SAMN06469835 |
| SRA |
SRX2600473 |
| 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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