Project description:This SuperSeries is composed of the following subset Series: GSE25275: Gene expression patterns of biopsies from a colonoscopy taken in 2007 of an ulcerative colitis patient infected with Trichuris trichiura GSE25276: Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura GSE25277: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura Refer to individual Series
Project description:Trichuris muris is very closely related to the human parasite T. trichiura sharing cross reactive antigens. Moreover, it is a remarkably tractable model system for dissecting immune responses and host parasite relationships and is actively being investigated in a number of laboratories worldwide. T. muris is a naturally occurring nematode parasite of mice which resides in the caecum and colon and has a direct oral faecal life cycle. High-throughput sequencing of Trichuris muris transcriptome for de novo assembly of transcripts. The main objective of this project is to recognize genes expressed in given life stages. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans including invertebrates and vertebrates. In metazoa, DNA elimination occurs in somatic cells during early development leaving the germline genome intact. Because limited comprehensive analyses of the genome changes have been carried out and high quality reference genomes for organisms that undergo DNA elimination are not available, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum, and the horse parasite, Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the nematode parasite of humans, Ascaris lumbricoides, and a parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (~1,000-2,000 or 5-10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent Toxocara canis. Analysis of the chromosomal breakage regions suggests a sequence independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our chromosomal level genome assemblies and annotations provide comprehensive genomic resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies. Overall design: A total of 11 Ascaris samples are used for this study, including regions of the male germline (1, mitotic region; 2, spermatogenesis; 3, post-meiotic region; 4, seminal vesicle; and 5, spermatids), regions of the female germline (1, mitotic region; 2, early pachytene; 3, late pachytene; 4, diplotene; and 5, oocyte), and a mixed sample for 5'-end SL and TeloPrime RNA-seq.