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Sample GSM6742881 Query DataSets for GSM6742881
Status Public on Sep 29, 2023
Title MCP 1 [scRNA-seq]
Sample type SRA
 
Source name FACS sorted Tomato positive tumor cells
Organism Mus musculus
Characteristics cell type: FACS sorted Tomato positive tumor cells
genotype: Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
Extracted molecule total RNA
Extraction protocol For tumors, tumor samples were manually dissected from normal surrounding tissue.
For sorted cells, tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA extraction and library preparation was performed according to manufacturer's instructions (single cell 3' v3.1 protocol, 10x Genomics)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description MCP 375 - 2177143
Data processing The demultiplexing, 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)
Assembly: GRCm38(mm10)
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Nov 18, 2022
Last update date Sep 29, 2023
Contact name Hongjian Jin
E-mail(s) hongjian.jin@STJUDE.ORG
Organization name St Jude Children's Research Hospital
Department Center for Applied Bioinformatics
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38015
Country USA
 
Platform ID GPL24247
Series (2)
GSE218274 PAX3-FOXO1 expression in endothelial progenitors dictates myogenic reprogramming and rhabdomyosarcoma identity
GSE218358 PAX3-FOXO1 drives tumor formation from multiple lineages [scRNA-seq]
Relations
BioSample SAMN31792225
SRA SRX18313018

Supplementary file Size Download File type/resource
GSM6742881_2177143_MEH324.tar.gz 63.5 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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