 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 06, 2022 |
| Title |
High-throughput muscle fiber typing from RNA sequencing data |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Skeletal muscle fiber type distribution has implications for human health, muscle function and performance. This knowledge has been gathered using labor intensive and costly methodology that limited these studies. Here we present a method based on muscle tissue RNA sequencing data (totRNAseq) to estimate the distribution of skeletal muscle fiber types from frozen human samples, allowing for larger number of individuals to be tested. By using single-nuclei snRNA sequencing (snRNAseq) data as a reference, cluster expression signatures were produced by averaging gene expression of cluster gene markers and then applying these to totRNAseq data and inferring muscle fiber nuclei type via linear matrix decomposition. This estimate was then compared with fiber type distribution measured by ATPas staining or myosin heavy chain protein isoform distribution of 62 muscle samples in two independent cohorts (n = 39 and 22). The correlation between the sequencing-based method and the other two were rATPas = 0.65 [0.46 – 0.84], [95% CI] and rmyosin = 0.80 [0.71 – 0.89], with p = 7.96 x 10-6 and 8.06 x 10-6 respectively. The deconvolution inference of fiber type composition was accurate even for very low totRNAseq sequencing depths, i.e., down to an average of ~5.000 paired end reads. This new method consequently allows for measurement of fiber type distribution of a larger number of samples using totRNAseq in a cost and labor efficient way. For the first time it is now feasible to study the association between fiber type distribution and health outcomes in large well-powered studies.
|
| |
|
| Overall design |
snRNAseq data from 1 human and 1 chimpanzee skeletal muscle sample
|
| |
|
| Contributor(s) |
Oskolkov N, Hansson O, Pääbo S, Camp G, Ström K |
| Citation(s) |
35780170 |
| |
| Submission date |
Dec 08, 2021 |
| Last update date |
Jul 06, 2022 |
| Contact name |
Nikolay Oskolkov |
| E-mail(s) |
nikolay.oskolkov@scilifelab.se
|
| Phone |
0761463349
|
| Organization name |
Lund University
|
| Street address |
Sölvegatan 35
|
| City |
Lund |
| ZIP/Postal code |
22657 |
| Country |
Sweden |
| |
|
| Platforms (1) |
| GPL31050 |
Illumina HiSeq 2000 (Homo sapiens; Pan troglodytes) |
|
| Samples (2) |
|
| Relations |
| BioProject |
PRJNA787279 |
| SRA |
SRP349855 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190489_SkeletalMuscle_HumanChimp_10X.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
| GSE190489_cell_barcodes.txt.gz |
66.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
