|
| Status |
Public on Sep 29, 2023 |
| Title |
aP2-Cre Tomato+ 2 [scRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted tomato positive cells from the sternocleidomastoid muscle
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FACS sorted tomato positive cells from the sternocleidomastoid muscle
genotype: aP2-Cre;R26-tdTomato
|
| 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 |
adult ATOM male tom+ SCM - 2122763
|
| 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 |
SAMN31792215 |
| SRA |
SRX18313028 |
