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| Status |
Public on Aug 22, 2024 |
| Title |
mouse, skeletal muscle, Mbnl1KO, rep3 |
| 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,Mbnl1{delta}E3/{delta}E3 Mbnl2+/+
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 |
S779Nr6.1
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| Data processing |
Adapter clipping with an in-house Python script, and redundant reads were removed with a fastx_collapser tool from the FASTX-Toolkit package.
The reads in FASTA format were then mapped against a set of mouse pre-miRNA sequences obtained from the miRBase 21 database using Megablast from the BLAST package, version 2.2.26.
It was required that the reads mapped in a sense orientation with no mismatches over the full read length. Then, using an in-house Python script, miRNA expression levels were calculated in the following way: raw counts of all reads mapped to a pre-miRNA sequence in a region occupied by an annotated mature miRNA +/- 2 nt were summed.
The raw expression values served as input for subsequent differential expression analysis with DESeq2 using default settings with a threshold of an adjusted P value below 0.05.
Assembly: mouse pre-miRNA sequences obtained from the miRBase 21 database
Supplementary files format and content: Tab-separated text file containing raw reads 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) |
| GSE245814 |
MBNL splicing factors regulate the microtranscriptome of skeletal muscles (mouse, skeletal muscle, Mbnl-KO panel) |
| GSE245818 |
MBNL splicing factors regulate the microtranscriptome of skeletal muscles |
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| Relations |
| BioSample |
SAMN37885561 |
| SRA |
SRX22147032 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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