biostudies-arrayexpressEvangelos ProkakisMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14986This analysis identifies genes which are affected upon irradiationbiostudies-arrayexpressSequencing - Single-end (50 bp) sequencing was performed at the Transcriptome and Genome Analysis Laboratory (TAL), Göttingen, Germany, using HiSeq 4000 (Illumina®).Nucleic Acid Extraction - RNA from WAP-T NP8 mammary carcinomas were extracted using a Trizol/Chloroform protocol according to manufacturer's instructions. For this purpose, shock-frozen mammary tumors from female mice were used, which were stored at -80 °C. To extract the RNA, approximately 40 mg of frozen tissue was cut for each condition on a dry ice-cooled block with a scalpel. Experiments were conducted with two untreated tumor tissues and four irradiated tumors. All utensils used for the preparation were disinfected with 70 % DEPC-EtOH. Tissues were collected in separate tissue-homogenization tubes filled with 1,4 mm ceramic beads. All the following steps were carried out on ice. 1 ml (EXTRAzol) reagent was added, and the tissues were dissociated in the tissue lyser for three cycles 20 s at 50 Hz and 30 s break on ice. After centrifugation (12.000 x g, 1 min, 4 °C), the supernatant was transferred to new tubes and the samples were incubated for 5 min at RT to dissociate the nucleotide complexes. For phase separation, 200 μl chloroform was added and the tubes were vortexed for 15 s. The lysate was incubated at RT for 10 min, followed by centrifugation (12.000 x g, 10 min, 4°C). The resulting upper aqueous phase containing the RNAs was transferred to a new 1,5 ml tube and the second round of chloroform extraction was performed, adding again 200 μl chloroform, incubating 5min at RT, centrifuging (12.000 x g, 5 min, 4 °C) and transferring the upper phase to a new 1,5 ml tube. The fresh tubes with 500 μl isopropanol and the upper phases were strongly mixed and incubated at -80 °C for at least 1h to precipitate the RNA. After centrifugation (12.000 x g, 10 min, 4 °C), the supernatant was discarded and the RNA pellet was washed with 80 % ice-cold EtOH (centrifugation 12.000 x g, 10 min, 4°C) and was centrifuged again (8000 x g, 1 min, 4 °C) before air drying to remove excess EtOH. The RNA pellet was resuspended in 50 μl DEPC-H2O and RNA concentration was measured with DeNovix Spectrophotometer. To improve the quality of the mentioned RNA, a second cycle of RNA isolation was performed, following all the above-mentioned steps for EXTRAzol/Chloroform extraction.Library Construction - For sequencing, mRNA libraries were generated using the NEXTflex Rapid Directional RNA-Seq Library Prep Kit (Bioo Scientific, Austin, TX, US) and sequenced in a HiSeq 4000 automatic sequencer (Illumina, San Diego, CA, US). Total RNA was converted into a library of template molecules suitable for Illumina sequencing using TruSeq RNA Sample Prep kit v2 (Illumina) according to the manufacturer´s instructions adapted for half-volume reactions. Library quality was assessed using an Agilent Bioanalyzer 2100.Sample Collection - H8N8-derived mammary tumors were dissected from WAP-T mice and snap-frozen at liquid nitrogen.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - mRNA-seq data quality was checked using the FastQC Read Quality reports (Galaxy Version 0.72). Sequences were trimmed up to 11 bases from the 5´end with the \"Trim leading or trailing characters\" tool (Galaxy Version 0.0.1). All sequences were allocated to the mouse genome (Mus_musculus.GRCm38) and aligned using the RNA STAR gapped-read mapper for RNAseq data (Galaxy Version 2.5.2b-2). To quantify the gene sequence fragments (reads) which were allocated to a gene of the reference mouse genome, featureCounts (Galaxy Version 1.6.0.2) was utilized.Data Transformation - Differential gene expression analysis and normalization were performed using the Galaxy Deseq2 (2.11.40.6+galaxy1) application.UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 4000RNA-seq of coding RNAMus musculusEvangelos ProkakisfalsemRNA-seq of H8N8 derived mammary tumors, untreated (Ctr.) or upon 11 Gy total dose (Rad.)This analysis identifies genes which are affected upon irradiation2026-03-13T00:00:00Z2026-03-13T02:02:31.223Z2025-03-27T22:55:56.136ZE-MTAB-14986ERP170938EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184