{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Amy Webb"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16126"],"description":["Functional lysosomes are essential for tumor growth. CQ, a widely used lysosome inhibitor, has been combined with various other therapeutics for testing in cancer patients. However, no studies have reported enhanced antitumor effects from these treatments. To investigate how tumor cells survive CQ-mediated lysosome inhibition, we conducted transcriptome analysis using RNA sequencing (RNA-seq) on  a NSCLC H1299 cell line to compare gene expression changes between control (vehicle) and CQ treatment groups."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA libraries for RNA-seq were prepared using SMARTER Mrna-SEQ Library Prep Kit following manufactures's protocols.","Sample Collection - 3X105 H1299 cells were cultured in RPMI-1640 medium containing 10% FBS for 24 hours. The medium was then replaced with fresh RPMI-1640 supplemented with 1% FBS, 5 mM glucose, 4 mM glutamine, and 10 µM CQ for an additional 24 hours.","Sequencing - Sequenced on Illumina NovaSeq 6000 across 2 lanes","Nucleic Acid Extraction - RNA was harvested using Rneasy mini plus kit (Qiagen), 2 µg of total RNA was used for the construction of sequencing libraries.","Growth Protocol - H1299 cells were maintained in RPMI-1640 medium supplemented with 10%FBS and in humidified atmosphere with 5%CO2 at 37°C."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads normalized using variance stabilizing transformation from deseq2","Sequence Alignment - Raw fastq mapped to human reference genome GRCh38 using hisat2.  Gene counts generated by featureCounts for genes annotated by ensembl GRCh38 v101"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Yaogang Zhong","Deliang Guo","Amy Webb"],"additional_accession":[]},"is_claimable":false,"name":"RNA sequencing of non–small cell lung cancer (NSCLC) cell line H1299 following chloroquine (CQ) treatment","description":"Functional lysosomes are essential for tumor growth. CQ, a widely used lysosome inhibitor, has been combined with various other therapeutics for testing in cancer patients. However, no studies have reported enhanced antitumor effects from these treatments. To investigate how tumor cells survive CQ-mediated lysosome inhibition, we conducted transcriptome analysis using RNA sequencing (RNA-seq) on  a NSCLC H1299 cell line to compare gene expression changes between control (vehicle) and CQ treatment groups.","dates":{"release":"2025-12-05T00:00:00Z","modification":"2025-12-05T20:22:13.716Z","creation":"2025-11-13T18:19:16.589Z"},"accession":"E-MTAB-16126","cross_references":{"ENA":["ERP184368"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}