ZF 96 Pooled BACs
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR009067_1.fastq.gz | Fastqsanger.gz | |||
| ERR009067_2.fastq.gz | Fastqsanger.gz | |||
| ERR009068_1.fastq.gz | Fastqsanger.gz | |||
| ERR009068_2.fastq.gz | Fastqsanger.gz | |||
| ERR009069_1.fastq.gz | Fastqsanger.gz |
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Project description:Sequencing of Zebrafish mapped clones in non-indexed pools using the Illumina Genome Analyzer
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Project description:This experiment was conducted as part of an overall study aimed at examining effects of a dopamine receptor antagonist on reproduction, behavior, and gene expression in cyprinid fish. Relative to gene expression, we hypothesized that if haloperidol disrupted normal regulation of the HPG axis, there may be robust transcriptional alterations in the ovary of exposed females that might serve as useful markers of exposure and/or effects. For the purposes of this study, robust transcriptional alterations were defined as those detected in two separate fish species (fathead minnow and zebrafish), exposed to the same concentration of haloperidol for the same duration. There is a companion fathead minnow microarray experiment (GSE15115) that these data are compared to. Transcriptional responses in the ovary of the two species are compared in terms of differentially expressed genes, enriched gene ontology categories they represent, and associated pathways.
2009-12-22 | GSE14861 | GEO
Project description:A strategy is presented to select, pool and spot human BAC clones on an array in such a way that each spot contains five well performing BAC clones, covering one chromosome arm. A mini-array of 240 spots was prepared representing all human chromosome arms in a 5-fold as well as some controls, and used for comparative genomic hybridization (CGH) of 10 cell lines with aneusomies frequently found in clinical cytogenetics and oncology. Spot-to-spot variation within five replicates was below 6% and all expected abnormalities were detected 100% correctly. Sensitivity was such that replacing one BAC clone in a given spot of five by a BAC clone from another chromosome, thus resulting in a change in ratio of 20%, was reproducibly detected. Incubation time of the mini-array was varied and the fluorescently labelled target DNA was diluted. Typically, aneusomies could be detected using 30 ng of non-amplified random primed labelled DNA amounts in a 4 h hybridization reaction. Potential application of these mini-arrays for genomic profiling of disseminated tumour cells or of blastomeres for preimplantation genetic diagnosis, using specially designed DNA amplification methods, are discussed.
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Project description:mRNA expression analysis of 4 different pools of medulloblastoma samples with characteristic cytogenetic aberrations Keywords: Genetic modification
2010-07-09 | GSE22823 | GEO
Project description:Minor histocompatibility (H) antigens are the molecular targets of allo-immunity responsible both for the development of anti-tumor effects and for graft-versus-host disease (GVHD) in allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, despite their potential clinical use, our knowledge of human minor H antigens is largely limited by the lack of efficient methods of their characterization. Here we report a robust and efficient method of minor H gene discovery that combines whole genome association scans (WGAS) with cytotoxic T-lymphocyte (CTL) assays, in which the genetic loci of minor H genes recognized by the CTL clones are precisely identified using pooled-DNA analysis of immortalized lymphoblastoid cell lines with/without susceptibility to those CTLs. Using this method, we have successfully mapped two loci: one previously characterized (HMSD encoding ACC-6), and one novel. The novel minor H antigen encoded by the BCL2A1 was identified within a 26 kb linkage disequilibrium block on chromosome 15q25, which had been directly mapped by WGAS. The pool size required to identify these regions was no more than 100 individuals. Thus, once CTL clones are generated, this method should substantially facilitate discovery of minor H antigens applicable to targeted allo-immune therapies and also contribute to our understanding of human allo-immunity. Keywords: pooled DNA, minor histocompatibility antigen, genotype array For CTL-2A12, we collected 44 cytotoxicity-positive (CTX+) and 44 cytotoxicity-negative (CTX-) B-LCLs. For CTL-1B9, 57 CTX+ and 38 CTX- B-LCLs were collected. Pools of DNA were generated and subjected to analysis on Affymetrix® GeneChip® 100K and 500K microarrays in duplicates.Genetic mapping of the minor H locus was performed by identifying marker SNPs that showed statistically significant deviations in allele-frequencies between CTX+ and CTX- pools based on the observed allele-specific signals in the microarray experiments.
2007-12-31 | E-GEOD-10044 | biostudies-arrayexpress
Project description:We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.
2020-11-21 | GSE161907 | GEO
Project description:Sequence-based mapping of Schistosoma mansoni pooled BACs
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Project description:BACKGROUND: BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. RESULTS: This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. CONCLUSIONS: Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.
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Project description:In frame of the IBSC The Genome Analysis Centre (TGAC) sequenced BACs, that constitute the MTP of barley using MatePair Pool Sequencing. The BAC Pools presented here could not be assigned to any barley chromosome and were therefore assinged 0H.
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