Project description:The present study used CRISPR/Cas9 technology to generate two knockout strains of salmon by mutating 1) all fads genes simultaneously (delta-5fad, delta-6fad-a, delta-6fad-b and delta-6fad-c), and 2) delta-6fad-b and delta-6fad-c genes. Liver was taken and RNA-seq was used.
Project description:Farmed and wild Atlantic salmon was given either vegetable oil (low DHA and EPA) feed or fish oil (high in DHA and EPA) feed or phospholipid (high in phospholipid) feed from start of feeding. We sampled and RNAseq two tissues (pyloric caeca and liver) on day 0, day 48, day 65 and day 94 after initial feeding.
Project description:The experiment focused on the transcriptomic changes associated with gill inflammation in sea farmed Atlantic salmon (Salmo salar). To ensure the multifactorial aspect of gill inflammation, fish were sampled at three marine production sites (A on Isle of Mull, B in Shetland and C in Shetland) between October 2017 and March 2018. All fish were of strain Fanad and originated from the same egg fertilisation batch. They were reared in different hatcheries (Couldoran, Pettigo-Damph and Knock-Frisa for sites A, B and C, respectively) for one year and entered the sea in spring 2017. The resultant gill tissues (44 samples in total with 1 gill sample per fish) were first scored for proliferative gill disease (PGD), using gross morphology PGD scores from 0 with no visual pathology to 5 with severe visual pathology, and then subjected to RNA-seq and histopathological (microscopic) examination. One RNA-seq sample (fish 95) was identified as an outlier and removed from the subsequent analysis. As a result, the analysis aiming to integrate gill transcriptome, gross morphology and histopathology was performed on 43 gill samples, classified either as PGD score 1 (n = 26) or PGD score 3 (n = 17). In total, 20 gill samples originated from site A (10 with PGD1 and 10 with PGD 3, 10 samples from site B (7 with PGD1 and 3 with PGD 3) and 13 samples from site C (9 with PGD1 and 4 with PGD 3).
Project description:Purpose: Celiac disease (CD) is a risk factor for developing Small Bowel Carcinoma (SBC) with a 14 folds higher risk than that of the general population. As SBCs associated with CD (CD-SBCs) are extremely rare, very few molecular data are currently available about their pathogenesis and information about CD-SBC transcriptomic profiling is completely lacking. Patients and Methods: We generated RNA-seq data on 13 CD-SBCs selected from the largest and well-characterized series of CD-SBCs published so far that was collected by the Small Bowel Cancer Italian Consortium. In all cases we compared the CD-SBC transcriptional signatures with the four consensus molecular subtypes (CMS) of colorectal carcinoma (CRC) applying the ‘CMS classifier’. CpG Island Methylator Phenotype (CIMP+) was evaluated in all cases using methylation-sensitive multiple ligation-dependent probe amplification. Results: RNA-based signatures of CD-SBCs exhibited strong similarities with CRCs. Twelve of 13 CD-SBCs (92%) fell within the two main subtypes exhibiting high immune and inflammatory signatures, i.e. CMS1 and CMS4. CMS1 CD-SBCs (62% of cases) were commonly MSI/CIMP+ tumors and showed increased expression of genes associated with a diffuse TH1 and cytotoxic T immune infiltrate, up-regulation of apoptosis, cell cycle progression and proteasome pathways. CMS4 CD-SBCs (31% of cases) showed prominent TGF-β activation and were characterized by complement-associated inflammation, matrix remodeling, stromal invasion and angiogenesis Conclusions: RNA-based signatures of CD-SBCs strongly recapitulate CMS classification of CRC, give a promising tool to improve our knowledge of this rare entity and provide clinically useful information using the wealth of data available for CRC.
Project description:We have infected the model legume Medicago truncatula with Meloidogyne hapla and harvested tissue over a time course. Transcriptome sequencing was performed on each sample using the Illumina RNA-Seq method. [Longitudinal Experiment] RNA was isolated from M. hapla eggs and pre-penetration juveniles (J2) and also from a time course of M. truncatula infected with M. hapla J2 at five time points: 1, 2, 4, 5, and 7 days after inoculation (DAI). Roots (local) and shoots (global) tissues from infected and uninfected plants were sampled. Each sample was loaded on five lanes for sequencing. Collectively, 22 samples were generated in total from - M. hapla egg and J2 (two samples), - infected M. truncatula root 1-2-4-5-7 DAI (five samples), - infected M. truncatula shoot 1-2-4-5-7 DAI (five samples), - uninfected M. truncatula root 1-2-4-5-7 DAI (five samples), - and uninfected M. truncatula shoot 1-2-4-5-7 DAI (five samples). Thus, 110 fastq files (= 22 samples x 5 lanes). [Diunrnal Experiment] M. truncatula roots inoculated with M. hapla was sampled at 6 time-points: 22:30, 2:00, 5:00, 6:30, 14:00, and 21:00. Lighting was turned off at 22:00 and turned on at 06:00. Four biological replicates were taken for each time point, providing 24 samples in total. Thus, 24 fastq files (= 6 time points x 4 replicates).
Project description:To assess expression of mtDNA genes in the canine transmissible venereal tumour (CTVT), biopsy tissue samples from 33 CTVT cases were subjected to total RNA extraction, and stranded RNA sequencing libraries generated with the Ribo-Zero ribosomal RNA removal kit (insert size 100–300 bp) were sequenced using 75-bp paired-end sequencing reads on an Illumina HiSeq4000 instrument. Gene transcript abundance was quantified using the Salmon software (v0.8.2).
Project description:The aim of the present study was to identify a pediatric inflamatory bowel disease (pIBD) characteristic microRNA profile serving as potential Crohns disease and ulcerative colitis specific diagnostic pattern and to further analyze the related target genes. Illumina small RNA sequencing was performed on inflamed and intact colonic biopsies of Crohn's disease and control patients. Selected miRs were further investigated by real-time reverse transcription (RT)-PCR. To analyze network connection of differentially expressed miRs and their target genes the MiRTarBase database and previous transcriptome sequencing data were used. We demonstrated a characteristic colonic miR pattern in pIBD that could facilitate deeper understanding of the pathomechanism of IBD and may serve as a diagnostic tool in the future.