{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Nicholas Rajan"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14645"],"description":["This dataset comprises RNA sequencing data generated from salivary samples as part of the study titled \\\\\"Characterizing the Salivary RNA Landscape to Identify Potential Diagnostic, Prognostic, and Follow-Up Biomarkers for Breast Cancer.\\\\\" The dataset includes single-end RNA-seq reads stored in FASTA format, derived from three sample groups: breast cancer patients (BC), healthy controls (CRL), and follow-up samples from treated breast cancer patients (FL). Each sample file is annotated with metadata containing information on sample type and anonymized patient IDs. The data captures both coding and long non-coding RNAs extracted from saliva, providing a comprehensive profile of the salivary RNA landscape. The primary goal of this dataset is to facilitate the identification of RNA biomarkers with potential diagnostic, prognostic, and treatment monitoring applications in breast cancer."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Unstimulated saliva samples were collected from breast cancer (BC) patients and healthy individuals using DNA Genotek collection tubes (Ref CP-190). Participants were instructed to avoid eating, drinking, smoking, or oral hygiene activities for at least 30 minutes before collection to reduce variability in saliva composition. Each saliva-filled tube was shaken vigorously for at least 8 seconds to ensure sample homogeneity.","Nucleic Acid Extraction - In their original collection vials, samples were incubated at 50°C for 1 hour in a water bath. After incubation, samples were aliquoted into 1 ml portions in separate microcentrifuge tubes for storage at –80°C. Saliva samples were thawed on ice, and a 0.5 mL aliquot was incubated at 90°C for 15 minutes to inactivate RNases, then cooled to room temperature. A neutralizer solution (20 μL, 1:25) was added to the saliva aliquot, followed by a 10-minute incubation on ice. Samples were then centrifuged at maximum speed for 3 minutes. The supernatant was carefully transferred to a fresh 5 mL tube without disturbing the pellet. The samples were then stored at -80 awaiting further RNA extraction. RNA was isolated from cell-free saliva samples using the miRNeasy Serum/Plasma Advanced Kit (Qiagen Cat no: 217184), following the manufacturer’s protocol with slight modifications. To each sample, 2.5 mL of QIAzol lysis reagent was added, and the mixture was vortexed to ensure thorough lysis, followed by a 5-minute incubation at room temperature. Tubes were capped, vortexed for 15 seconds, incubated at room temperature for 2–3 minutes, and centrifuged at 12,000 x g at 4°C for 15 minutes. The upper aqueous phase was carefully transferred to a new 5 mL tube, avoiding contamination from the interphase, and mixed with 1.5 volumes of 100% (final volume ~5 mL). For RNA purification, the sample was loaded in 700 μL aliquots, onto an RNeasy MinElute spin column connected to a Vac-Man® Laboratory Vacuum Manifold. The vacuum was opened carefully. The process was repeated until the entire sample was loaded. The column was then removed from the vacuum manifold, placed in a 2 mL collection tube, and washed with 700 μL Buffer RWT, followed by centrifugation at ≥8000 x g for 15 seconds. The column was subsequently washed with 500 μL Buffer RPE and centrifuged at ≥8000 x g for 15 seconds, followed by a final wash with 500 μL of 80% ethanol and centrifugation at ≥8000 x g for 2 minutes at room temperature. The column was transferred to a fresh 2 mL collection tube with the lid open and centrifuged at full speed for 5 minutes to dry the membrane. Finally, the column was placed into a new 1.5 mL collection tube, and RNA was eluted by applying 30 μL of RNase-free water directly to the center of the membrane, followed by centrifugation at full speed for 1 minute.","Sequencing - Quantified libraries were pooled and sequenced on Illumina platforms with a single-end read length of 50 base pairs. Sequencing was conducted without mRNA selection, ensuring an unbiased representation of all RNA species present in the samples.","Library Construction - RNA sequencing was performed at Novogene (Cambridge, United Kingdom). First-strand cDNA synthesis was carried out using random hexamer primers, followed by second-strand cDNA synthesis using either dUTP for directional libraries or dTTP for non-directional libraries."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500","DNA Genotek collection tubes (Ref CP-190)","miRNeasy Serum/Plasma Advanced Kit","Illumina"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Characterizing the salivary RNA landscape to identify potential diagnostic, prognostic and follow-up biomarkers for breast cancer."],"pubmed_authors":["Nicholas Rajan","Rajan Nicholas1,*, Primac Irina1, Etlioglu Emre1, Debruyne Laurens 2, Janssen Ann1, Sallam Magy1, Tabury Kevin1, Quintens Roel1, Wiebren Tjalma2, Benotmane Mohammed Abderrafi 1,*"],"additional_accession":[]},"is_claimable":false,"name":"Characterizing the salivary RNA landscape to identify potential diagnostic, prognostic and follow-up biomarkers for breast cancer","description":"This dataset comprises RNA sequencing data generated from salivary samples as part of the study titled \\\\\"Characterizing the Salivary RNA Landscape to Identify Potential Diagnostic, Prognostic, and Follow-Up Biomarkers for Breast Cancer.\\\\\" The dataset includes single-end RNA-seq reads stored in FASTA format, derived from three sample groups: breast cancer patients (BC), healthy controls (CRL), and follow-up samples from treated breast cancer patients (FL). Each sample file is annotated with metadata containing information on sample type and anonymized patient IDs. The data captures both coding and long non-coding RNAs extracted from saliva, providing a comprehensive profile of the salivary RNA landscape. The primary goal of this dataset is to facilitate the identification of RNA biomarkers with potential diagnostic, prognostic, and treatment monitoring applications in breast cancer.","dates":{"release":"2025-07-01T00:00:00Z","modification":"2025-06-30T13:01:18.253Z","creation":"2024-11-28T17:21:03.592Z"},"accession":"E-MTAB-14645","cross_references":{"ENA":["ERP166632"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0004184"]}}