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Sample GSM3436818 Query DataSets for GSM3436818
Status Public on Feb 13, 2019
Title Adult satellite cells single-cell RNA-Seq
Sample type SRA
 
Source name mouse Tibialis anterior
Organism Mus musculus
Characteristics strain: Pax7-ZsGreen
cell type: mouse myogenic progenitors
age: 3 months-old
Growth protocol iPax3/iPax7 myogenic progenitors were generated thorugh sorting of Vcam1+Flk1- cells from EBs, plated and expanded upon Dox and bFGF administration for 3 passages, then collected with PBS-based dissociation buffer and submitted for downstream analyses.
Extracted molecule total RNA
Extraction protocol Cultured Cells and freshly sorted tissue-derived cells were lysated with buffer RA1+TCEP of kit RNA XS (Machirey-Nagel) and RNA was extracted according to manufacturer's instructions.
Libraries were prepared using Illumina standard protocols (RNA-Seq); Chromium Single Cell 3’ Reagent kit 10X Genomics (single-cell RNA-Seq)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description single-cell Sat
Data processing Illumina Casava 1.8 software used for basecalling.
libraries were aggregated and normalized via cellranger aggr function (--id=cellranger-aggr --csv=metadata.csv) using cellranger version 2.2.0. The output cloupe.cloupe file was imported into Loupe? Cell Browser (10X Genomics) version 2.0.0 and clusters were classified based on cell type.
Differential gene expression was determined via two methods: 1) Globally Distinguishing: for each selected cluster or group in a category, genes that distinguish that cluster from every other cell in the dataset were identified and 2) Locally Distinguishing: for each checked cluster or group, genes that distinguish that cluster from the other currently checked clusters in that category.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include aggregated gene expression matrix and differential gene expression results.
 
Submission date Oct 18, 2018
Last update date Feb 13, 2019
Contact name Tania Incitti
E-mail(s) tincitti@umn.edu
Organization name University of Minnesota
Street address 2231 6th Street SE
City Minneapolis
State/province Minnesota
ZIP/Postal code 55455
Country USA
 
Platform ID GPL17021
Series (2)
GSE121469 Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment [RNA-seq]
GSE121639 Pluripotent stem cell-derived myogenic progenitors remodel their molecular signature upon in vivo engraftment
Relations
BioSample SAMN10258822
SRA SRX4905902

Supplementary file Size Download File type/resource
GSM3436818_single-cell_Sat_barcodes.tsv.gz 2.2 Mb (ftp)(http) TSV
GSM3436818_single-cell_Sat_differential_expression.csv.gz 350.0 Kb (ftp)(http) CSV
GSM3436818_single-cell_Sat_genes.tsv.gz 217.5 Kb (ftp)(http) TSV
GSM3436818_single-cell_Sat_matrix.mtx.gz 6.3 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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