 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 29, 2023 |
| Title |
TCP 2 |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted Tomato positive tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FACS sorted Tomato positive tumor cells
genotype: Tek-Cre;Cdkn2a(Flox/Flox);Pax(3P3F/P3F);R26-tdTom (TCP)
|
| 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 from tumors was harvested using miRNeasy mini plus kit (Qiagen) and RNA from sorted cells was harvested using miRNeasy micro kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
TPIT 56 - 1955372
|
| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60), mapped to human (hg38) or mouse (mm10) genome assembly (STAR v2.7.1a).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (human release 31 for human sampls or mouse release 22 for mouse samples).
Assembly: hg38 for human samples and mm10 for mouse samples
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM text file
|
| |
|
| 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 |
| GSE218357 |
PAX3-FOXO1 drives tumor formation from multiple lineages [RNA-seq] |
|
| Relations |
| BioSample |
SAMN31792198 |
| SRA |
SRX18312860 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6742851_1955372_MEH204_TPIT-56.RSEM.genes.counts.txt.gz |
627.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
