GSE147127
GSE GEOSingle-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers
Organism:
Mus musculus
Platform:
GPL24247
Samples:
6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted:
Mar 17 2020
Last Updated:
Aug 09 2022
Status:
Public on Oct 11 2020
Contact:
Nathan,,Salomonis (Cincinnati Children's Hospital)
Relations
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA613077
SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP253104
Summary
While the majority of cells contain a single nucleus, cell types such as trophoblasts, osteoclasts, and skeletal myofibers require multinucleation. One advantage of multinucleation can be the assignment of distinct functions to different nuclei, but comprehensive interrogation of transcriptional heterogeneity within multinucleated tissues has been challenging due to the presence of a shared cytoplasm. Here, we utilized single-nucleus RNA-sequencing (snRNA-seq) to determine the extent of transcriptional diversity within multinucleated skeletal myofibers. Nuclei from mouse skeletal muscle were profiled across the lifespan, which revealed the emergence of distinct myonuclear populations in postnatal development and their reactivation in aging muscle. Our datasets also provided a platform for discovery of novel genes associated with rare specialized regions of the muscle cell, including markers of the myotendinous junction and functionally validated factors expressed at the neuromuscular junction. These findings reveal that myonuclei within syncytial muscle fibers possess distinct transcriptional profiles that regulate muscle biology.
Overall Design
Single-nucleus RNA-seq of tibialis anteior muscle of BL6 wild-type mice across the lifespan: 10 days, 21 days, 5 months (TA and soleus), 24 months, 30 months
Analysis (5 steps)
View Data Processing
Processing steps for GSE147127
- Raw sequencing data of all samples were processed using the cellRanger workflow (version 3.1.0), using a combined intron-exon reference produced as described using the vendor-provided âGenerating a Cell Ranger compatible "pre-mRNA" Reference Packageâ guidelines (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
- In brief, the âpre-mRNAâ reference was derived using the default exon-level GTF file provided by 10x Genomics (Â http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-mm10-3.0.0.tar.gz).
- Using the below awk command, this exon-level GTF file into âpre-MRNAâ GTF containing intron transcript definitions).
- Next, the below mkref command was run to produce the final âpre-MRNAâ GTF and genome fasta file ($ cellranger mkref --genome=Mmpre --fasta=genome.fa --genes=genes.premrna.gtf).
- For each dataset, we corrected for ambient background RNA by filtering with the R package SoupX (version 0.3.0), using the inferNonExpressedGenes() function to determine which genes had the highest probability of being ambient mRNA, and the strainCells() function in order to transform count matrices.
Supplementary Files (1)
GSE147127_RAW.tar
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GEO Samples (6)
Dataset Citations (1)
SRA Experiments (6) and Runs (12)
Total: 155312 MBGSM4418991: WT tibialis anterior 24 months 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330487
BioProject: PRJNA613077
BioSample: SAMN14392086
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: 24 months
sequencing parameters: 434 million reads
Original files (1)
Tibialis anterior muscle
GSM4418992: C57BL/6 WT tibialis anterior 5 months 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330488
BioProject: PRJNA613077
BioSample: SAMN14392085
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: 5 months
sequencing parameters: 419 million reads
Original files (1)
Tibialis anterior muscle
GSM4418993: C57BL/6 WT tibialis anterior 30 months 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330489
BioProject: PRJNA613077
BioSample: SAMN14392084
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: 30 months
sequencing parameters: 474 million reads
Original files (1)
Tibialis anterior muscle
GSM4418994: C57BL/6 WT tibialis anterior postnatal day 10 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330490
BioProject: PRJNA613077
BioSample: SAMN14392083
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: day 10
sequencing parameters: 1,013 million reads
Original files (1)
Tibialis anterior muscle
GSM4418995: C57BL/6 WT tibialis anterior postnatal day 21 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330491
BioProject: PRJNA613077
BioSample: SAMN14392082
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Tibialis anterior muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: day 21
sequencing parameters: 433 million reads
Original files (1)
Tibialis anterior muscle
GSM4418996: C57BL/6 WT soleus 5 months 10X snRNA-seq; Mus musculus; RNA-Seq
Sample: SRS6330492
BioProject: PRJNA613077
BioSample: SAMN14392081
Platform: ILLUMINA
Instrument: Illumina NovaSeq 6000
Organism: Mus musculus
Sample attributes
source_name: Soleus muscle
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: 5 months
sequencing parameters: 356 million reads
Original files (1)
Soleus muscle
Linked Publications (1)
Zfp697 is an RNA-binding protein that regulates skeletal muscle inflammation and remodeling.
Proceedings of the National Academy of Sciences of the United States of America · 2024
Data Files (12)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | 10X-Millay-30-Month-20190812-3v3mm_S6_L001_I1_001.fast… | RNA-Seq | 12.6 GB | link | |||
| — | 10X-Millay-30-Month-20190812-3v3mm_S6_L002_I1_001.fast… | RNA-Seq | 12.6 GB | link | |||
| — | 10X_Millay_Aging_20190326_3v3mm_S3_L001_I1_001.fastq.gz | RNA-Seq | 11.6 GB | link | |||
| — | 10X_Millay_Aging_20190326_3v3mm_S3_L002_I1_001.fastq.gz | RNA-Seq | 11.5 GB | link | |||
| — | 10X-Millay-P10-20191120-3v3mm_S1_L001_I1_001.fastq.gz | RNA-Seq | 19.0 GB | link | |||
| — | 10X-Millay-P10-20191120-3v3mm_S1_L002_I1_001.fastq.gz | RNA-Seq | 19.1 GB | link | |||
| — | 10X-Millay-P21-20190513-3v3mm_S10_L001_I1_001.fastq.gz | RNA-Seq | 11.7 GB | link | |||
| — | 10X-Millay-P21-20190513-3v3mm_S10_L002_I1_001.fastq.gz | RNA-Seq | 11.7 GB | link | |||
| — | 10X-Millay-Soleus-20190826-3v3mm_S6_L001_I1_001.fastq.… | RNA-Seq | 9.7 GB | link | |||
| — | 10X-Millay-Soleus-20190826-3v3mm_S6_L002_I1_001.fastq.… | RNA-Seq | 9.7 GB | link | |||
| — | 10X-Millay-WT-Muscle-20190131-3v3_S10_L001_I1_001.fast… | RNA-Seq | 11.2 GB | link | |||
| — | 10X-Millay-WT-Muscle-20190131-3v3_S10_L002_I1_001.fast… | RNA-Seq | 11.2 GB | link |