{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Olivier Gandrillon"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16963"],"description":["A GRN inference algorithm identified the KO of TCF4 as an important dynamical player in neuroblastomas tumoroids. JQ1 treatment is supposed to mimic in silico the KO of TCF4. Retinoic acid is supposed to induce forced differentiation of neuroblastomas."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - 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.","Library Construction - 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)","Sequencing - Librairies were sequenced on the NextSeq500 platform (paired-end, 25/0/0/67).","Sample Collection - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The  expression matrix that was normalized using median count depth normalization with log1p transformation."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Olivier Gandrillon"],"additional_accession":[]},"is_claimable":false,"name":"scRNA of neuroblastomas tumoroids treated, or not, with ether JQ1 or retinoic acid","description":"A GRN inference algorithm identified the KO of TCF4 as an important dynamical player in neuroblastomas tumoroids. JQ1 treatment is supposed to mimic in silico the KO of TCF4. Retinoic acid is supposed to induce forced differentiation of neuroblastomas.","dates":{"release":"2026-07-07T00:00:00Z","modification":"2026-07-07T05:24:43.667Z","creation":"2026-04-27T15:51:20.147Z"},"accession":"E-MTAB-16963","cross_references":{"ENA":["ERP192691"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}