2025-05-25
ENA first public
ERC000011
ENA-CHECKLIST
Lund University - Translational Cancer Research
INSDC center name
public
INSDC status
ERS23301518
SRA accession
E-MTAB-14846:DMSO_2_S2
Submitter Id
ArrayExpress
broker name
LU-NB-2
cell_line
Relapsed tumor
cell_type
not collected
collection date
human
common name
Protocols: Following the treatment period, cell pellets were collected by centrifugation. The samples were flash-frozen and stored at -80°C to preserve RNA integrity until further processing.  Cells were cultured and passaged as described (Persson et al., PMID: 28860499). LU-NB-2 PDX cells were seeded in T25 flasks (1milion cells per condition) and allowed to grow for 24 hours.  Following the initial growth period, LU-NB-2 PDX cells were treated for 48 hours with one of the following conditions: a combination of PCZ+PIT (1.6 µM + 6.7 µM, n = 4), PCZ alone (1.6 µM; n = 4), PIT alone (6.7 µM; n = 4), or DMSO as a vehicle control (1% v/v, n = 4). Two biological replicates were performed resulting in a total of 8 samples per each condition. Notably, treatment with the combination of PCZ and PIT led to an approximately 15% reduction in neuroblastoma cell viability compared to controls.  Total RNA was extracted from the collected cell pellets using the AllPrep DNA/RNA Mini Kit (80204, Qiagen), following the manufacturer’s instructions. RNA quality and concentration were assessed before library preparation. RNA quality was evaluated using the Agilent RNA ScreenTape Assay (G2991-90020 Rev. B) on the TapeStation 4200 System (Agilent), while RNA concentration was measured with the QuantIT RNA HS Assay Kit (Q33140, Life Technologies) using the Qubit Flex Fluorometer (Q33327, Invitrogen Thermo Fisher Scientific).  Approximately 500 ng of total RNA was used for mRNA library preparation. Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (20020594, Illumina) following the TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E). The libraries were indexed with IDT for Illumina TruSeq RNA UD Indexes (20022371, Illumina) and subjected to 13 PCR cycles. Cleanup steps were automated on a KingFisher FLEX system (Thermo Scientific), and incubations and PCR were performed using an Eppendorf Mastercycler X50s (Eppendorf). Library concentrations were measured using the QuantIT 1X dsDNA HS Assay Kit (Q33232, Invitrogen) on a Qubit Flex Fluorometer (Q33327, Invitrogen Thermo Fisher Scientific). The Agilent D5000 ScreenTape System (G2964-90050 Rev. B) assessed library size and quality on the TapeStation 4200 System (Agilent).
description
Undifferentiated
developmental stage
neuroblastoma
disease
MYCNamp, 1p-,17q+
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Homo sapiens
organism
Homo sapiens
organism
brain metastasis
organism part
Homo sapiens
scientific_name
DMSO_2_S2
title