biostudies-arrayexpressJeffrey IshizukaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15926MCC13 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).biostudies-arrayexpressSample 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData 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.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensJeffrey IshizukafalsePerturbational sequencing of patient tumors reveals midkine as an innate immune checkpoint in neuroendocrine tumorsMCC13 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).2025-11-24T00:00:00Z2026-05-30T15:30:20.462Z2025-10-29T17:04:42.521ZE-MTAB-15926ERP183318EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0003969EFO_0004184