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Status |
Public on Sep 29, 2023 |
Title |
MCP 1 [scRNA-seq] |
Sample type |
SRA |
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Source name |
FACS sorted Tomato positive tumor cells
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Organism |
Mus musculus |
Characteristics |
cell type: FACS sorted Tomato positive tumor cells genotype: Myf6-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (MCP)
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
MCP 375 - 2177143
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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
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Submission date |
Nov 18, 2022 |
Last update date |
Sep 29, 2023 |
Contact name |
Hongjian Jin |
E-mail(s) |
hongjian.jin@STJUDE.ORG
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Organization name |
St Jude Children's Research Hospital
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Department |
Center for Applied Bioinformatics
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Street address |
262 Danny Thomas Place
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City |
Memphis |
State/province |
TN |
ZIP/Postal code |
38015 |
Country |
USA |
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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] |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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