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Sample GSM6341891 Query DataSets for GSM6341891
Status Public on May 05, 2023
Title Muscle, control,3 samples pooled, scRNA-seq
Sample type SRA
 
Source name Skeletal muscle
Organism Homo sapiens
Characteristics tissue: Skeletal muscle
cell line: primary cells
cell type: Myogenic cells
genotype: healthy control individuals (2 males, one female)
treatment: NA
Treatment protocol NA
Growth protocol Muscle biopsies from controls and DM1 patients were minced, digested in collagenase, and plated in a culture dish. Myoblasts were grown in Sk-MAX media complemented with Sk-MAX supplement and 20% fetal bovine serum (FBS). Myoblasts were expanded for a few days until there were enough cells for purification by FACS (Using anti-CD56 as positive myogenic marker and 7-AAD for cell viability).
Extracted molecule total RNA
Extraction protocol Myogenic cells total RNA was extracted with Qiazol reagent according to the manufacturer’s specifications
Single cell suspensions of myogenic cells were resuspended in PBS containing 0.04% ultra-pure BSA. scRNAseq libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. Generated libraries were sequenced on an Illumina HiSeq4000.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 10x Genomics
Data processing The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
DoubletFinder was used to identify putative doublets in each DGE matrix relying solely on gene expression data.
Assembly: GRCh38- 2020-A
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Jul 18, 2022
Last update date May 05, 2023
Contact name Mohan Malleshaiah
E-mail(s) mohan.malleshaiah@ircm.qc.ca
Organization name Montreal Clinical Research Institute (IRCM)
Department stem cells and cellular reprogramming
Lab Dr. Malleshaiah
Street address 110 Pine Avenue West
City Montreal
State/province Quebec
ZIP/Postal code H2W 1R7
Country Canada
 
Platform ID GPL20301
Series (1)
GSE208360 Clearance of defective muscle stem cells by senolytics reduces the expression of senescence-associated secretory phenotype and restores myogenesis in myotonic dystrophy type 1
Relations
BioSample SAMN29793818
SRA SRX16314692

Supplementary file Size Download File type/resource
GSM6341891_Control_barcodes.tsv.gz 10.4 Kb (ftp)(http) TSV
GSM6341891_Control_features.tsv.gz 325.6 Kb (ftp)(http) TSV
GSM6341891_Control_matrix.mtx.gz 47.2 Mb (ftp)(http) MTX
GSM6341891_ctrl_final.rds.gz 100.5 Mb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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