{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Emre Taylan Duman"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16218"],"description":["Lung adenocarcinoma (LUAD) exhibits wide variability in radiotherapy response, yet no validated biomarkers currently guide radiation stratification. The ataxia-telangiectasia mutated (ATM) kinase plays a central role in DNA damage repair, and its loss has been associated with radiosensitivity. This study aimed to identify molecular determinants of radiosensitivity in LUAD and to evaluate the impact of ATM status and pharmacological ATM inhibition on radiation response. Radiosensitivity of five LUAD cell lines was assessed using clonogenic, MTS, and impedance-based assays. The selective ATM inhibitor AZD1390 was used to test radiosensitization in ATM-proficient versus ATM-deficient models. Transcriptomic and proteomic profiles after irradiation (2 Gy) were analyzed by RNA sequencing and dat"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - cDNA libraries were sequenced by using an S2 flow cell NovaSeq6000; 100 cycles, 20-25 Mio reads/sample.","Sample Treatment - Samples were transported in a thermo-insulated container and irradiated with 6 MV photons at a dose of 2 Gy using a Clinac 2300 C/D linear accelerator (Varian). Non-irradiated controls were transported in parallel under identical conditions.","Nucleic Acid Extraction - Following 15 min incubation, 200 µl chloroform were added, and the mixture was gently inverted to mix phase. After centrifugation (12,000 rpm, 15 min, 4 °C), the aqueous phase was transferred to a fresh reaction tube, and RNA was precipitated by addition of 500 µl isopropanol. After centrifugation under the same conditions, the supernatant was discarded, and the pellet was air-dried. RNA was resuspended in RNase-free water and quantified spectrophotometrically.","Library Construction - RNA quality was assessed by measuring the RNA integrity number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.). Library preparation for RNA-Seq was performed in the STAR Hamilton NGS automation using the Illumina Stranded mRNA Prep (Cat.N° 20040534) and the ID for Illumina RNA UD Indexes Set A, Ligation with 96 Indexes (Cat. N° 20091646) starting from 300 ng of total RNA. The size range of the final cDNA libraries was determined by applying the SS NGS Fragment 1- to 6000-bp Kit on the Fragment Analyzer (average 340 bp). Accurate quantification of cDNA libraries was performed by using the DeNovix DS-Series System.","Sample Collection - Flasks were washed with 2*5ml ice-cold PBS, then cells were scraped with 2 ml ice-cold PBS and were sedemented by centrifugation (500xg, 15 min, 4 °C).","Growth Protocol - Cells were seeded 2 days before experiemtna and were grown in RPMI with 10 % FCS supplemented with Glutamax, Penicilin and Streptomycin at 37 °C and 5 % CO2 in humidified atmosphere."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Reads were aligned to the human reference genome (GRCh38) using STAR aligner v2.7.10 and annotated with the Ensembl GTF file (release 110).","Data Transformation - Gene-level counts were summarized with featureCounts v1.6.3, and transcript-based counts were normalized using the DESeq2 R package. Pairwise differential gene expression analysis was performed in DESeq2, applying Benjamini-Hochberg multiple testing correction."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Anna Luisa Riedl","Emre Taylan Duman","Hanibal Bohnenberger"],"additional_accession":[]},"is_claimable":false,"name":"Toward biomarker-guided radiotherapy: Multi-omics analysis links ATM status to radioresistance in lung adenocarcinoma","description":"Lung adenocarcinoma (LUAD) exhibits wide variability in radiotherapy response, yet no validated biomarkers currently guide radiation stratification. The ataxia-telangiectasia mutated (ATM) kinase plays a central role in DNA damage repair, and its loss has been associated with radiosensitivity. This study aimed to identify molecular determinants of radiosensitivity in LUAD and to evaluate the impact of ATM status and pharmacological ATM inhibition on radiation response. Radiosensitivity of five LUAD cell lines was assessed using clonogenic, MTS, and impedance-based assays. The selective ATM inhibitor AZD1390 was used to test radiosensitization in ATM-proficient versus ATM-deficient models. Transcriptomic and proteomic profiles after irradiation (2 Gy) were analyzed by RNA sequencing and dat","dates":{"release":"2026-08-30T00:00:00Z","modification":"2026-08-30T01:00:48.652Z","creation":"2025-11-20T09:26:04.721Z"},"accession":"E-MTAB-16218","cross_references":{"ENA":["ERP185391"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}