Homo sapiens
Protocols: PDTs were derived as described in : \"Nguyen, T. N. T., et al. (2025). Multiscale modeling of the spatial structure of stem cells in neuroblastoma patient-derived tumoroids reveals a critical role for a short range diffusive process. BioRXiv\"  Single-cell RNA sequencing was performed using RevGel-seq (Komatsu, 2023), adapted by Scipio Bioscience. PDTs were trypsinized into a single-cell suspension and chemically labeled with a bifunctional linker (polyA and hydrophobic moiety) in DPBS for 5 minutes. Labeled cells (300 cells/µL, 15,000 total) were mixed with barcoded beads (50 µL each) and homogenized to form cell-bead complexes via collisions. The mixture was diluted in 2.4 mL hydrogel, gelated on ice for 20 minutes, and lysed to release RNA, which hybridized to bead-bound poly-T oligos.  After degelation, bead-bound RNA underwent reverse transcription (Maxima H Minus RT kit) and second-strand synthesis (S3 Supermix). cDNA was PCR-amplified (KAPA HiFi), purified with SPRIselect, and quality-checked via TapeStation and Qubit. Libraries were prepared using the Illumina Nextera XT Kit (5-minute fragmentation, 10 PCR cycles) and sequenced on the NextSeq500 platform (paired-end, 25/0/0/67).
ENA first public
2026-07-08
INSDC center name
LBMC - ENS de Lyon
INSDC status
public
Submitter Id
E-MTAB-16741:Sample 2
age
15
broker name
ArrayExpress
collection date
not collected
common name
human
disease
neuroblastoma
geographic location (country and/or sea)
not collected
isolate
not applicable
organism part
patient-derived tumoroid
replicate
EV226
sample name
E-MTAB-16741:Sample 2
scientific_name
Homo sapiens
sex
male