biostudies-arrayexpressSandra Ramirez Caleromixed samplehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15157RNA sequencing paired-end data. This study involves Corallium rubrum, with data of two populations from contrasting environments (shallow vs mesophotic), exposed to a control and a temperature stress treatment in a common garden experiment. RNAseq samples were taken every 5 days from each individual. This experiment includes the following design: Shallow Population (15-18m): Shallow (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates Deep Population (48m): Mesophotic (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates N=18 replicates in each condition, for a total of N = 36 replicates for the total study.biostudies-arrayexpressSequencing - Sequencing was performed on the NovaSeq 6000 platform (Illumina) in paired-end mode with a read length of 2 × 151 bp, generating 40–60 million reads per library. Sequencing followed the manufacturer’s protocol for dual indexing. Image analysis, base calling, and quality scoring were processed using Real-Time Analysis (RTA) software version 3.4.4, with FASTQ files generated as the final output.Sample Collection - Six adult colonies were randomly collected from two populations at different depths with contrasting thermal regimes along the Catalonian coast (Spain; Figure 1a). The first population was sampled (N=3 colonies) at 15 m depth at Cap Castell (3°13'10.233\" N, 42°4'56.276\" E), while the second population was sampled (N=3 colonies) at 48 m depth at Pota del Llop (3°13'33.787\" N, 42°2'52.736\" E). The six experimental replicates from each individual were divided into two treatments (3 replicates each): a control (18°C) and a stress (25°C), following a common garden experimental set-up for ten days. For the stress treatment, the temperature was increased stepwise from 18°C to 25°C over three days and maintained at 25°C until the end of the experiment. Fragments of C. rubrum were sampled threefold for RNA sequencing during the initial day of the experiment (T0), day 5th (T5), and day 10th (T10) in the two treatments (control and stress) and stored in RNAlater at -20°C.Nucleic Acid Extraction - RNA extractions were conducted using the RNAeasy Mini Kit protocol (Qiagen) with a modification of the lysis step that involved smashing the tissue with a sterile cane in TRIzol™ (Thermo-Scientific). The resulting RNA was quantified using the Qubit® RNA BR Assay Kit (Thermo Fisher Scientific), while quality was assessed using the RNA Integrity Number (RIN), obtained on a Fragment Analyzer system, using the DNF-471 RNA kit (Agilent). Samples with a RIN > 6 were retained.Library Construction - mRNA-focused sequencing libraries were prepared using the KAPA Stranded mRNA-Seq Kit for Illumina Platforms (Roche), following manufacturer’s recommendations, starting with 500 ng of total RNA. Illumina-compatible adapters with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated to the RNA fragments. The ligation products were enriched via 15 cycles of PCR. The final libraries were validated using the DNA 7500 Assay on an Agilent Bioanalyzer 2100 system.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw read quality was examined using FastQC, then reads were trimmed and adapters were removed using Trimmomatic, potential fungal, bacterial, and viral contamination was removed with Kraken. de novo transcriptome assembly was created using reads from all six colonies with trinity. Assembly statistics were obtained using trinity script TrinityStats.pl. Quality of assembly was checked using Bowtie2, transdecoder, and BLASTX (Swissprot/Uniprot database). We addressed the completeness of our assembly using BUSCO and the Nx statistics.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAmixed sampleSneha SureshJoaquim GarrabouMarta GutMarc JouSandra Ramirez CaleroMikel ZabalaJean-Baptiste LedouxXenia SarropoulouPaula Lopez-SendinofalseLocal adaptation patterns in red coral populations subjected to climate change using transcriptomicsRNA sequencing paired-end data. This study involves Corallium rubrum, with data of two populations from contrasting environments (shallow vs mesophotic), exposed to a control and a temperature stress treatment in a common garden experiment. RNAseq samples were taken every 5 days from each individual. This experiment includes the following design: Shallow Population (15-18m): Shallow (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates Deep Population (48m): Mesophotic (N=3 individuals)x 3T (T0, T5, T10) = 9 replicates N=18 replicates in each condition, for a total of N = 36 replicates for the total study.2025-11-01T00:00:00Z2025-11-01T10:00:50.02Z2025-05-20T10:53:15.874ZE-MTAB-15157ERP172750EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184