Zebrafish brachyury chipseq
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina Genome Analyzer II, Illumina Genome Analyzer
ORGANISM(S): Danio rerio
SUBMITTER:
PROVIDER: E-ERAD-28 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:ChIP sequencing of chordoma UCH-1 cell line. A well characterised chordoma cell line which bears all the morphological and immunohistochemical features of a chordoma (large vacuolated slow-growing cells, brachyury and cytokeratin-positive) have been used in this study. Chromatin immunoprecipitation using a well characterised anti-Brachyury antibody which has been used in immunohistochemistry of chordoma samples and previous ChIP studies in other systems. 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/
2011-10-17 | E-ERAD-23 | biostudies-arrayexpress
Project description:During early stages of embryonic development the genome is transcriptionally inactive and cells are under the control of maternally provided mRNA and proteins. At a key point in development, known as the maternal to zygotic transition (MZT), the genome becomes activated and the maternally provided mRNAs begin to degrade. In the early zebrafish embryo, when under maternal control, cells divide rapidly and synchronously with cell cycles that lack gap phases. At cell cycle ten the introduction of gap phases lengthens the cell cycle and synchronised division is lost. During the MZT, zygotic activation of microRNAs leads to the targeted degradation of a number of maternally provided mRNAs, thus linking genome activation to maternal mRNA degredation.While the MZT has been studied in several different organisms the molecular mechanisms that coordinate genome activity and mRNA degradation remain largely unknown. For example, while the bulk of zygotic transcription occurs at cell cycle ten we do not understand why there is a minor wave of transcription before this time point. Similarly maternal mRNAs degrade at different rates, with only a percentage undergoing microRNA-mediated degredation. The aparant different rates of maternal mRNA degredation may be obscured by zygotic transcription.In order to gain an understanding of the MZT I intend to establish a precise understanding of transcription in the early embryo by using solexa sequencing to perform transcript counting at five different developmental stages that span the MZT. Specifically I intend to use crosses from two different zebrafish strains SAT (Sequenced AB and Tbingen, Zv9) and WIK. This project will allow one to understand the overall transcription profiles of genes in the early embryo, but importantly, the SNPs between the two different strains will determine if transcripts are maternal or zygotic (paternal). As a proof of principle we will first use one lane of sequencing to identify transcripts from a cross of an SAT and a WIK fish. This will allow us to observe SNPs between the two different strains. This will be run over one solexa lane. We will then sequence from five different time points on four different crosses SAT male and WIK female, WIK male and SAT female, WIK male and WIK female and SAT male with SAT female. We will prepare the libraries, which will be sequenced paired-end 54 bp over a total of seven lanes of solexa.. 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/
2012-03-12 | E-ERAD-57 | biostudies-arrayexpress
Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. This was used to generate mutant and wild type RNA libraries for solexa sequencing. The sequencing data will be compared to isolate changes that may be caused by loss of rax activity. The RNA samples were extracted with Trizol, then were DNAse treated following the Invitrogen DNAse I protocol and re-precipitated with ethanol. 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/
2013-01-08 | E-ERAD-130 | biostudies-arrayexpress
Project description:Strongyloides ratti is a common gastro-intestinal parasite of the rat. The adult parasites are female only, about 2mm long and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. In the environment infective larval stages develop either directly or after a facultative sexual free-living adult generation. Infective larvae infect hosts by skin penetration.S. ratti is the laboratory analogue of the parasite of humans, S. stercoralis. S. stercoralis is a wide-spread parasite of humans, occurring principally in the tropics and sub-tropics: some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates. As part of the Strongyloides ratti genome project we are profiling the transcriptome of the parasite across its life cycle using RNA-Seq.. 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/
2013-01-28 | E-ERAD-92 | biostudies-arrayexpress
Project description:RNA-Seq from lymphoblastoid cell lines for Gorilla, chimpanzee and bonobo species. This RNA-Seq data has been described in the following article: Scally et al., Nature 2012;483;7388;169-75, DOI: 10.1038/nature10842, and its further analysis can be freely submitted for publication. For information on the proper use of data shared by the Wellcome Trust Sanger Institute (including information on acknowledgement), please see http://www.sanger.ac.uk/datasharing/>
2013-01-09 | E-ERAD-129 | biostudies-arrayexpress
Project description:The main objective of this project is to recognize genes expressed in the life stages and tissue types of a variety of different cestode species, including Echinococcus multilocularis, E. granulosus, Hymenolepis microstoma, H. nana and others. 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/
2013-02-28 | E-ERAD-50 | biostudies-arrayexpress
Project description:We have recently identified BCL11A as a key regulator of mammary stem (MaSC) and progenitor cells. Deletion of BCL11A in MaSC leads to loss of ability of those cells to engraft a cleared mammary fatpad. This biological function of BCL11A correlates with its overexpression in basal breast cancers which are thought to arise from stem and progenitor subtypes. Basal breast cancer cell lines where BCL11A is knocked down using shRNA failed to develop tumours in xenograft transplantations in mice. Therefore, BCL11A is potentially a novel target for breast cancer treatment. Microarray analysis has identified potential gene targets for BCL11A however, it is not known if these targets are directly regulated by BCL11A at the transcription level. We would like to perform CHIP-SEQ analysis on a mammary cell line using BCL11A antibody under two conditions (normal expression and overexpression of BCL11A).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/protocol to be provided
2013-01-28 | E-ERAD-69 | biostudies-arrayexpress
Project description:Trypanosoma vivax is a major pathogen of domestic cattle and wildlife across sub-Saharan Africa. For many years, the WTSI has had a research interest in developing a genome sequence for T. vivax, as part of a wider programme concerning African trypanosome parasites of Humans and animals. In 2012 a draft genome sequence for T. vivax Y486 was published by the WTSI and our collaborators in comparison with related species, T. brucei and T. congolense. This study identified numerous putative genes in T. vivax that have no known affinity and are therefore species-specific. A related transcriptomic study confirmed that some of these putative genes are transcribed, but lacked accuracy and was based on a single parasite life stage only. Until recently, it has not been possible to culture different T. vivax life stages in refined media. There is now the opportunity to use new approaches to produce whole cell RNA for both insect and bloodstream parasite stages. We sequence stage-specific cDNA and identify stage-specific genes, and compare these features with similar data already available for T. brucei and T. congolense, which display substantial differences in their developmental cycles. 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/
2013-03-07 | E-ERAD-100 | biostudies-arrayexpress
Project description:This study focuses on epigenetic reprogramming in the mouse germ line: DNA methylation marks, including those of imprinted genes, are thought to be erased between E11.5 and E13.5 in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. DNA methylation patterns are then re-established during the de novo methylation phase in the male germ line several days later (around E15.5) and in the female germ line after birth during adult life. Epigenetic reprogramming in PGCs is poorly understood mainly because of the technical challenges that arise from very low cell numbers in the embryo. The aim of this study is to create genome-wide maps of DNA methylation patterns of male and female PGCs at crucial time points during epigenetic reprogramming and to investigate the changes in those profiles on a single-gene level. We have already successfully prepared and sequenced the first set of BS-Seq libraries of PGCs with Illumina's GAIIx platform. From this, we gained significant insight into the global DNA methylation levels and methylation patterns over multy-copy-loci such as repeat elements. In order further enhance our analysis and finish this project for publication, it is crucial to increase the genomic coverage of our datasets. This will also allow us to link the BS-Seq data with other MeDIP-Seq and RNA-Seq datasets that have already been created in this study.Protocol: Input DNA was sonicated using a Bioruptor UCD-200 (Diagenode) to a final size distribution of 300bp 1000bp. End-repair and A-tailing were performed with the NEBNext DNA Sample Prep Master Mix Set 1. Illuminas Early Access Methylation Adaptor Oligo Kit was used for the adapter ligation. The adapter-ligated DNA was treated with sodium-bisulfite using the Imprint DNA Modification Kit from Sigma-Aldrich according to the manufacturers instructions for the two-step protocol. After the clean up, the bisulfite-treated DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase from Agilent with 18 cycles of amplification. The entire PCR reaction was run on a 1.5% agarose TBE gel and size selection was performed for DNA fragments between 200bp 250bp. DNA from the excised gel piece was purified with the Qiagen Gel Extraction Kit.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/
2013-01-07 | E-ERAD-48 | biostudies-arrayexpress
Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including important human pathogens. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages of the mouse malaria parasite, P. chabaudi AS. The aim is to analyse cir gene expression during Plasmodium chabaudi infection and determine whether host genetic background can influence cir expression. 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/. Abstract: Transcriptome sequencing of blood stage P. chabaudi AS parasites grown under different host genetic backgrounds.
2011-11-03 | E-ERAD-25 | biostudies-arrayexpress