title: T7
organism: Homo sapiens
description: Protocols: Treatment was administered for 10 days, after which mice were euthanized, and tumor pieces were resected and snap-frozen. RNA was extracted from snap-frozen tumor pieces stored at -80°C to preserve RNA integrity until further processing.  Neuroblastoma in vivo model of LU-NB-1 was obtained via subcutaneous injection of human high-risk, MYCN-amplified neuroblastoma organoids in NSG mice (PDX, LU-NB-1). When tumors reached 200-300 mm3, mice were randomized into treatment groups: control (n=7), PCZ + PIT combination (n=7), and PCZ + PIT combination + COJEC (n=6).  PCZ + PIT (total volume 50 μl; 5 mg/kg of each drug) was administered i.t. daily five times per week. COJEC treatment was given i.p. and consisted of five different chemotherapies distributed in cycles over one week; Day 1 – cisplatin (1mg/kg) + vincristine (0,25mg/kg), Day 3 – etoposide (4mg/kg) + cyclophosphamide (75mg/kg), Day 5 – carboplatin (25mg/kg). All COJEC drugs were dissolved in saline and combination treatment was suspended in vehicle consisting of 2.5% DMSO, 2.5% Tween 80, 40% PEG, 55% PBS solution. Control mice were treated with i.t. injections of the vehicle used for PCZ+PIT and i.p injections of saline. Mouse weights and tumor volumes were measured three times per week throughout the study.  Tumor pieces were cut to a maximum of 3x3 mm on ice and then kept overnight at -20°C in RNAlater™-ICE transition solution (AM7030, Invitrogen). Total RNA was extracted from the collected tumor pieces using Tissuelyzer (85600, Qiagen) followed by 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, Thermo Fisher Scientific) using the Qubit Flex Fluorometer (Q33327, Invitrogen Thermo Fisher Scientific).  Approximately 400 ng of total RNA was used for mRNA library preparation. Libraries were constructed using the Illumina® Stranded mRNA Prep, Ligation Kit (20040534, Illumina) following the Illumina Stranded mRNA Prep, Ligation Reference Guide (Document #1000000124518 v03), modification of “Enrich DNA Fragment” step: 12 PCR cycles. The libraries were indexed with Illumina® RNA UD Indexes Set A, Ligation (96 Indexes, 20091655, Illumina). Cleanup steps were automated on a KingFisher FLEX system (18-5400620, Thermo Scientific), and incubations and PCR were performed using an Eppendorf Mastercycler X50s (6311000010, Eppendorf). Library concentrations were measured using the QuantIT 1X dsDNA HS Assay Kit (Q33232, Thermo Fisher Scientific) on a Qubit Flex Fluorometer (Q33327, Invitrogen Thermo Fisher Scientific). Library size and quality were assessed using the Agilent D5000 ScreenTape System (5067- 5588, Agilent) on the TapeStation 4200 System (Agilent).
attributes.tag: ENA first public
attributes.value: 2025-05-30
attributes.tag: INSDC center name
attributes.value: Lund University - Translational Cancer Research
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-14902:T7
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: LU-NB-1
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: human
attributes.tag: disease
attributes.value: neuroblastoma
attributes.tag: genotype
attributes.value: MYCNamp, 1p-,17q+
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: adrenal gland
attributes.tag: sample name
attributes.value: E-MTAB-14902:T7
attributes.tag: sampling site
attributes.value: primary tumor
attributes.tag: scientific_name
attributes.value: Homo sapiens