{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14902"],"description":["Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, specially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of this experiment as to asses in vivo response of combination of Prochlorperazine and Pitavastatin alone or along standard of care chemotherapy COJEC. Neuroblastoma in vivo model 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. Treatment was administered for 10 days, after which mice were euthanized, tumor pieces were collected snap-frozen. Mouse weights and tumor volumes were measured three times per week throughout the study. RNA was extracted from snap-frozen tumor pieces and RNA sequencing was conducted."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 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.","Nucleic Acid Extraction - 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).","Sample Treatment - 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.","Sequencing - Prepared RNA libraries were pooled and diluted to a final concentration of 0.65 nM, with 1% PhiX Control(FC-110-3001, Illumina)  included in the pool. Sequencing was performed on a NovaSeq 6000 System (Illumina) at the Center for Translational Genomics, Lund University. Libraries were sequenced using the NovaSeq 6000 S1 Reagent Kit, 300 cycles v1.5 (20028317, Illumina), following the NovaSeq 6000 Sequencing System Guide (Document #1000000019358 v11). Paired-end reads were generated with a configuration of 150-10-10-150 bp.","Library Construction - 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)."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data Transformation - Transcript-level abundance estimates (TPM) were obtained from Kallisto during pseudoalignment. For downstream analyses, the pseudoalignment output files were summarized into gene-level counts using the tximport R package (v1.30.0; Soneson et al., 2015), with annotations derived from the Ensembl GRCh38 (v111) transcriptome via the biomaRt R package (v2.58.0; Durinck et al., 2009).    The gene-level count matrix was subsequently imported into a DESeqDataSet object and normalized using the DESeq2 package (v1.42.0; Love et al., 2014), which applies a median-of-ratios method to account for differences in sequencing depth and RNA composition. The regularized log transformation (rlog) was applied for exploratory data visualization, such as principal component analysis (PCA). However, differential expression analysis was performed using the DESeq2 normalization protocol as per the recommended workflow in the DESeq2 vignette.","Sequence Alignment - After trimming, sequencing reads were pseudoaligned using the Kallisto tool (v0.48.0; Bray et al., 2016). The pseudoalignment was performed against the GRCh38 (v111) Homo sapiens transcriptome obtained from the Ensembl database (Cunningham et al., 2022). The transcriptome index was generated using both the cDNA and ncRNA FASTA files to ensure comprehensive coverage of transcriptomic features."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"additional_accession":["ERP169872"],"pubmed_authors":["Erick Andrés Muciño Olmos"]},"is_claimable":false,"name":"RNA-seq of subcutaneous patient-derived neuroblastoma xenografts (LU-NB-1) - Comparison of Prochlorperazine + Pitavastatin (PCZ+PIT) combination alone to one combined with standard-of-care COJEC protocol (PCZ+PIT+COJEC)","description":"Neuroblastoma (NB) is a pediatric cancer characterized by significant heterogeneity and poor prognosis, specially in high-risk cases with MYCN amplification. Understanding the molecular response of neuroblastoma to different treatments can provide insights into potential therapeutic strategies. The aim of this experiment as to asses in vivo response of combination of Prochlorperazine and Pitavastatin alone or along standard of care chemotherapy COJEC. Neuroblastoma in vivo model 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. Treatment was administered for 10 days, after which mice were euthanized, tumor pieces were collected snap-frozen. Mouse weights and tumor volumes were measured three times per week throughout the study. RNA was extracted from snap-frozen tumor pieces and RNA sequencing was conducted.","dates":{"release":"2025-07-30T00:00:00Z","modification":"2026-05-30T16:30:20.259Z","creation":"2025-03-04T15:59:52.516Z"},"accession":"E-MTAB-14902","cross_references":{"ENA":["ERP169872"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}