{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lize Sels"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16125"],"description":["The aim of this experiment was to gain insights into temporal differences in gene expression following noise exposure in older adult mice with an average age of 17 months. Cochleae were collected at 24 hours, 72 hours and 1 week after noise exposure for subsequent RNA sequencing."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - After euthanasia, all cochleas were dissected using cold instruments under a binocular microscope. Next, they were rapidly put in RNAlater and stored at -80 C.","Library Construction - The RNA library preparation was performed using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt Set B1, combined with the QuantSeq-Flex First Strand Synthesis Module V2 to create longer fragments (Lexogen, Vienna, Austria). Before the library amplification PCR, the optimal PCR cycles were evaluated with the PCR Add-on and Reamplification Kit V2 (Lexogen, Vienna, Austria). The finalized cDNA libraries concentrations were measured using the Qubit high sensitivity dsDNA kit (Qubit 4.0, Thermo Scientific, Wilmington, USA). The fragment lengths, distribution and the quality of the libraries were evaluated using the D1000 ScreenTape assay (TapeStation, Agilent Technologies, Inc., Waldbronn, Germany). All libraries were then equimolar pooled.","Sequencing - The libraries were sent to the Centre of Medical Genetics Antwerp for single read sequencing with a minimum of 10M raw reads per sample on the NextSeq 500/550 (Illumina, Inc., San Diego, CA, USA). A first quality control of the raw sequencing data was performed by the Centre of Medical Genetics Antwerp.","Sample Treatment - The noise signal was generated using RPvdsEX software (Tucker-Davis Technologies, Alachua, FL, USA). The signal was routed through an attenuator and power amplifier (XPS-1200, Gemsound, New York, NY, USA) to a high-frequency tweeter speaker (HTH 8.7, Visaton, Haan, Germany). The noise exposure was performed in a ventilated soundproof box while the animals were awake and continuously being monitored via a webcam. Before the mice were exposed to noise, the sound levels were calibrated at several locations in the soundproof box to ensure uniformity of the stimulus. Across these measured sites within the chamber, the noise intensity varied by less or equal to 2dB. During the noise exposure, the animals were placed in a cage in the box at the locations of calibration so that the stimulus intensity was known for each animal individually.","Nucleic Acid Extraction - Afterwards, total RNA was isolated using the Rneasy mini kit® (Qiagen, Benelux, Belgium), according to the manufacturer’s protocol. Briefly, the cochlea was disrupted using a tissue homogenizer (Multipro, Dremel, Belgium) and lysate was homogenized with lysis buffer containing beta216 mercaptoethanol, followed by RNA extraction and purification using RNeasy mini spin columns. The concentration of the RNA samples was evaluated on the Qubit fluorometer 4.0, using the Qubit high sense RNA assay (Thermo Scientific, Wilmington, USA). The integrity and purity of the RNA samples was evaluated by the Agilent 4150 TapeStation System using the recommended RNA ScreenTape assay (Agilent Technologies, Inc., Waldbronn, Germany). For all samples, the RNA integrity number (RIN) values were above 7, indicating the superior quality of the isolated RNA."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Approximately 20-35 million 150 bp reads were obtained from all samples. After trimming the adapter sequences, low quality bases and very short reads, the resulting clean reads were aligned to the mouse reference genome Mus_musculus GRCm39 annotated with Ensembl version 106  238 and STAR 2.7.10.","Data Transformation - Quantification of the mapped reads was then performed with the program Featurecounts using the Subread package (31). Next, analysis of differentially expressed genes (DEGs) was performed using the package DESeq2."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 550"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Fien Aben","Dorien Verdoodt","Lize Sels"],"additional_accession":[]},"is_claimable":false,"name":"Time-series transcriptome analysis of the older adult mouse cochlea after noise exposure","description":"The aim of this experiment was to gain insights into temporal differences in gene expression following noise exposure in older adult mice with an average age of 17 months. Cochleae were collected at 24 hours, 72 hours and 1 week after noise exposure for subsequent RNA sequencing.","dates":{"release":"2025-11-21T00:00:00Z","modification":"2026-05-27T17:34:22.09Z","creation":"2025-11-14T15:21:40.47Z"},"accession":"E-MTAB-16125","cross_references":{"ENA":["ERP185099"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}