MASTIG
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Project description:Mastigamoeba balamuthi Raw sequence reads
| PRJNA724719 | ENA
Project description:An EST project for Mastigamoeba balamuthi has begun
| PRJNA12696 | ENA
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
2018-06-21 | GSE104355 | GEO
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
2018-06-21 | GSE104351 | GEO
Project description:Whole genome sequencing of 10 HCLc tumor and matched-germline T cells. Genomic DNA from highly purified HCLc tumor and T cell populations were utilized for library preparation using NEBNext Ultra DNA library prep kit. Sequencing was performed as 150 bp paired end sequencing using four lanes of an Illumina HiSeq4000 to an average depth of 12X. Reads from each library were aligned to the human reference genome GRCh37 using BWA-MEM (v0.7.12). The analysis of somatic genetic alterations in WGS data from tumor-germline pair HCLc samples was divided based on the nature of the mutation, as follow: single-nucleotide variants (SNVs), indels, CNAs and SVs. Moreover, COSMIC mutational signatures and subclonal architecture was inferred for each tumor.
2023-01-01 | E-MTAB-12046 | biostudies-arrayexpress
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:Adaptation of eukaryotic cells to anaerobic condition is reflected by deep changes in mitochondrial metabolism and their functional reduction. The most modified types of mitochondria are hydrogenosomes that generate molecular hydrogen with concomitant ATP synthesis and mitosome that completely lost energy metabolism. The reduction of mitochondria is associated with loss of peroxisomes that evolved from ER to compartmentalize pathways generating reactive oxygen species (ROS) and thus prevent cellular oxidative damage. Biogenesis and function of peroxisomes is tightly coupled with mitochondria. They share the fission machinery, pathways of oxidative metabolism, ROS scavenging, and metabolic products. The loss of peroxisomes in anaerobic eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in anaerobic, hydrogenosome bearing protist Mastigamoeba balamuthi. Initially, we identified conserved set of peroxisomal proteins peroxins that are required for protein import, peroxisomal growth and division. Key membrane associated peroxins (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles that were distinct from hydrogenosomes, ER and Golgi body. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) allows identification of 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed that they are specifically targeted to yeast peroxisomes. Matrix protein includes components of acyl CoA and carbohydrate metabolism, pyrimidine and CoA biosynthesis, whereas neither components of β-oxidation nor catalase were present. In conclusion, we identified new subclass of peroxisomes named “anaerobic” peroxisome that shifts the current paradigm and rises attention to reductive evolution of peroxisomes in anaerobic organisms.
2020-03-04 | PXD014205 | Pride