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| Status |
Public on Aug 22, 2024 |
| Title |
mouse, skeletal muscle, quadriceps, WT, postnatal day 90, rep1 |
| Sample type |
SRA |
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| Source name |
skeletal muscle, quadriceps
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| Organism |
Mus musculus |
| Characteristics |
tissue: skeletal muscle, quadriceps
genotype: C57BL/6J
age: 90 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from skeletal muscles in TRI reagent (Sigma) using a bead-based homogenizer (TissueLyser II, Qiagen) (2x 45 sec, max frequency) and 1.4-mm and 2.8-mm ceramic beads (Qiagen). Rapid RNA purification was performed using a Total RNA Zol-out kit (A&A Biotechnology) including DNase treatment according to the manufacturer’s protocol.
200 ng of total RNA was used to prepare libraries with a NEXTflex Small RNA-Seq Kit (Bioo Scientific)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S1615Nr16.1
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| Data processing |
Reads with lengths between 10 and 35 nt were selected with cutadapt (v1.18) for downstream analysis.
Raw reads were aligned to the Mus musculus genome (GRCm38 downloaded from the Ensembl database) with Bowtie2 (v2.4.1). The mapped reads were counted with featureCounts (v2.0.1) using the Mus musculus miRNA annotation file from mirBase, release version 22.
Differential expression of miRNAs was analyzed with the DESeq2 (v1.30.1) package using the likelihood ratio test (LRT) in R.
Assembly: Ensembl, GRCm38
Supplementary files format and content: Tab-separated text file containing raw counts for miRNA
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| Submission date |
Oct 19, 2023 |
| Last update date |
Aug 22, 2024 |
| Contact name |
Agnieszka Mykowska |
| E-mail(s) |
agamyk@amu.edu.pl
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| Organization name |
Adam Mickiewicz University
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| Street address |
Uniwersytetu Poznanskiego 6
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| City |
Poznan |
| ZIP/Postal code |
61-614 |
| Country |
Poland |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE245815 |
MBNL splicing factors regulate the microtranscriptome of skeletal muscles (mouse, skeletal muscle, developmental panel) |
| GSE245818 |
MBNL splicing factors regulate the microtranscriptome of skeletal muscles |
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| Relations |
| BioSample |
SAMN37885569 |
| SRA |
SRX22147045 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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