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ABSTRACT: Tasmanian devil gut microbiom post-translocation

PROVIDER: PRJNA540262 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8984600_1.fastq.gz	Fastqsanger.gz
	SRR8984600_2.fastq.gz	Fastqsanger.gz
	SRR8984610_1.fastq.gz	Fastqsanger.gz
	SRR8984610_2.fastq.gz	Fastqsanger.gz
	SRR8984620_1.fastq.gz	Fastqsanger.gz

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Project description:Tasmanian devil gut microbiom post-translocation

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The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer (small RNA sequencing)

Project description:The Tasmanian devil, a marsupial carnivore, is endangered due to the emergence of a clonally transmissible cancer known as Devil Facial Tumor Disease (DFTD). This fatal cancer is clonally derived and is an allograft transmitted between devils by biting. We performed a large-scale genetic analysis of DFTD with microsatellite genotyping, mitochondrial genome analysis, as well as deep sequencing of the DFTD transcriptome and miRNAs. These studies confirm that DFTD is a monophyletic clonally transmissible tumor, and suggest that the disease is of Schwann cell origin. On the basis of these results we have generated a diagnostic marker for DFTD, and identify a suite of genes of relevance to DFTD pathology and transmission. We provide a genomic dataset for the Tasmanian devil, which is applicable to cancer diagnosis, disease evolution and conservation biology. This submission contains only small RNA sequence data from this study. Small RNA (18 - 24 nt) sequences from 15 Tasmanian devil (Sarcophilus harrisii) tissue samples

2010-01-01 | E-GEOD-18352 | biostudies-arrayexpress

The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer (small RNA sequencing)

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Passage of transmissible cancers in the Tasmanian devil is due to a dominant, shared peptide motif and a limited repertoire of MHC-I allotypes

Project description:Transmissible cancers are spread via the passage of malignant cells. The survival of the Tasmanian devil, the largest marsupial carnivore, is threatened by two independent transmissible cancers, devil facial tumour (DFT) 1 and devil facial tumour 2 (DFT2). To aid the development of a peptide vaccine and to interrogate how histocompatibility barriers can be overcome, we analysed the peptides bound to Major Histocompatibility Complex class I molecules from the Tasmanian devil and its transmissible tumours.

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DNA methylation profile of Tasmanian Devil facial tumor biopsies and matched healthy skin and spleen samples, as well as additional nerve tissue, and strain 1 tumor cell line.

Project description:Purpose: Depict the landscape of epigenetic regulation in Tasmanian devil facial tumor biopsies. Differential analysis of healthy versus tumor biopsies highlighted 166 candidate genes with different DNA methylation levels in their promoters, which included the tumor-specific hypermethylated promoters of Estrogen Receptor 1 (ESR1) and the transcription factor GATA3.

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Project description:Tasmanian devil MHC typing

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Project description:The Tasmanian devil microbiome

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Tasmanian Devil Facial Tumour Disease - Imiquimod treatment of DFT1 cells

Project description:A Tasmanian Devil Facial Tumour Disease (DFTD) tumor cell line was treated with the drug Imiquimod

2018-04-12 | PXD007135 | Pride

Transcriptome profiling of Tasmanian Devil facial tumor (DFTD1) cell lines of 4 strains and the fibroblast cell line.

Project description:Purpose: To asses the transcriptome of 4 strains of the Tasmanian Devil facial tumor and one healthy fibroblast cell line. Methods: DFTD cells were grown from primary cell cultures derived from fine needle aspirates that have been collected from the wild. Total RNA from devil facial tumor strains 1-4 and the fibroblast was isolated from approximately 1 x 10^6 cells using QIAzol lysis reagent according to the manufacturer’s instructions (Qiagen). RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). The 5 libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 75 bp paired-end chemistry. Base calls provided by the Illumina Realtime Analysis software were converted into BAM format using Illumina2bam and demultiplexed using BamIndexDecoder. Paired-end reads were trimmed for adaptor sequences and filtered with the trimmomatic tool. Trimmed reads were aligned on the version 7.0 of the Tasmanian Devil with the STAR aligner. Counting of reads on annotated transcripts (Sarcophilus_harrisii.DEVIL7.0.90.gtf from Ensembl) was performed with featurecounts on fragments. The DESeq2 Biconductor library has been used for counts normalization and differential analysis between the transcriptomes of the four DFTD and fibroblast cell lines

2019-01-14 | GSE108107 | GEO

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