{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Jeffrey Ishizuka"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15926"],"description":["MCC13 MDK-WT and MDK-KO tumor cells were treated with IFNb for 24 hours and underwent bulk RNAseq. There are in total 4 conditions (control + no stim, control + IFNb, MDK-KO + no stim, MDK-KO + IFNb) and each condition has 3 biological replicates (except for control + no stim condition, due to poor quality, it only has two biological replicates)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Control and IFNb treated cells were harvested with trypsin.","Library Construction - 1 ug of RNA was submitted for construction of sequencing library.","Growth Protocol - 10x6 MCC13 MDK-WT and MDK-KO tumor cells were plated per 12-well plate of MCC13 MDK-WT and MDK-KO.","Nucleic Acid Extraction - RNA was harvested using Rneasy mini kit (Qiagen).","Sequencing - Illumina NovaSeq X Plus with 20 million read pairs per sample.","Sample Treatment - Cells were treated with 1000 IU/ml IFNb for 24 hours."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Salmon v1.4.0 was used to quantify the reads and generate TPM and raw counts matrices.","Sequence Alignment - Raw paired-end FASTQ files were quality-checked and trimmed with fastp v0.23.2. Trimmed reads were aligned to the human genome GRCh38.p14 with Salmon v1.4.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Jeffrey Ishizuka"],"additional_accession":[]},"is_claimable":false,"name":"Perturbational sequencing of patient tumors reveals midkine as an innate immune checkpoint in neuroendocrine tumors","description":"MCC13 MDK-WT and MDK-KO tumor cells were treated with IFNb for 24 hours and underwent bulk RNAseq. There are in total 4 conditions (control + no stim, control + IFNb, MDK-KO + no stim, MDK-KO + IFNb) and each condition has 3 biological replicates (except for control + no stim condition, due to poor quality, it only has two biological replicates).","dates":{"release":"2025-11-24T00:00:00Z","modification":"2026-05-30T15:30:20.462Z","creation":"2025-10-29T17:04:42.521Z"},"accession":"E-MTAB-15926","cross_references":{"ENA":["ERP183318"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0003969","EFO_0004184"]}}