Scaffolding Barley MTP BACs
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR599730_1.fastq.gz | Fastqsanger.gz | |||
| ERR599730_2.fastq.gz | Fastqsanger.gz | |||
| ERR599731_1.fastq.gz | Fastqsanger.gz | |||
| ERR599731_2.fastq.gz | Fastqsanger.gz | |||
| ERR599732_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 1364 |
Similar Datasets
Project description:In frame of the IBSC sequenced BACs from Barley, that constitute the MTP of barley.
| PRJEB13020 | ENA
Project description:BAC pool DNA hybridisation of barley to 44k Agilent microarrays. We have used two-channel Agilent expression microarrays to address thousands of gene sequences to individual BAC clones and contigs that form part of an emerging physical map of the large and unsequenced 5300 Mbp barley genome. By using two-colour processing, each array allows simultaneous co-hybridization of two independent BAC pools (SP), for which the data is analysed separately. As a general approach the method represents a cost-effective, highly parallel alternative to traditional gene-to-BAC addressing methods. By coupling the BAC address-data with gene-based genetic maps we were able to anchor thousands of BACs to the barley genetic map.
2010-12-02 | E-TABM-1017 | biostudies-arrayexpress
Project description:In frame of the IBSC The Genome Analysis Centre (TGAC) sequenced BACs, that constitute the MTP of barley chromosome 2H using Illumina 2000 chemistry.
| PRJEB11758 | ENA
Project description:In frame of the IBSC The Genome Analysis Centre (TGAC) sequenced BACs, that constitute the MTP of barley using Illumina 2000 chemistry. The BACs presented here could not be assigned to any barley chromosome yet and were therefore assigned as 0H.
| PRJEB11991 | ENA
Project description:Multi-targeting priming (MTP) for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences. We demonstrated superior performance of two MTPs compared to oligo-dT microarray profling and RNA tag sequencing the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development. Priming with MTPs in addition to oligo-dT resulted in higher sensitivity, a greater number of well-measured genes, more genes significantly differentially expressed, and a greater power to detect meager differences. Neurospora crassa mat A FGSC#2489 Three developmental stages and two different primers used for reverse transcription: mycelium oligo(dT) M1 protoperithecia oligo(dT) PP1 perithecia oligo(dT) PT1 mycelium oligo(dT)+ Multi-Targeted Primer [MTP] (M2) protoperithecia oligo(dT)+ MTP (PP2) perithecia oligo(dT)+ MTP (PT2)
2010-07-03 | E-GEOD-22658 | biostudies-arrayexpress
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.
| PRJEB11992 | ENA
Project description:Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing health concern. Better understanding of factors that prevent hepatic lipid accumulation may help design new strategies to prevent or treat MASLD. We have previously shown that adipocyte microsomal triglyceride transfer protein (MTP) regulates intracellular lipolysis by inhibiting adipose triglyceride lipase (ATGL) activity. Here, we show that adipose-specific MTP knockout mice (A-Mttp−/−) fed an obesogenic diet exhibit moderately high plasma triglyceride levels and less hepatic steatosis compared to their wild-type counterparts. Mechanistic studies revealed that high plasma triglycerides are due to increased hepatic triglyceride synthesis and production of triglyceride-rich lipoproteins from the livers of A-Mttp−/− mice. In addition, hepatocytes from these mice showed increased fatty acid oxidation and this could be a contributing factor for less hepatic steatosis. Studies aimed at understanding how adipose MTP regulated hepatic triglyceride-rich lipoprotein production and fatty acid oxidation revealed that adipose MTP modulates the release of agonists that activate hepatic PPARα activity. Our study highlights the significance of the regulated movement of fatty acid from adipose tissue to the liver in maintaining a healthy liver. It is likely that adipocyte fatty acid release can be modulated to reduce hepatic steatosis.
2025-12-09 | GSE280725 | GEO
Project description:To improve our understanding of the organization and evolution of the wheat gene space, we established the first map of genes of the wheat chromosome 1BS by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray (A-MEXP-2314) with 3D-pools of MTP BACs of from the 1BS physical map. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 1063 unigenes on the wheat chromosome 1BS BACs. By comparison with 454 sequences and Illumina survey sequence contigs from the sorted chromosome 1BS, we confirmed the assignation of 849 unigenes in individual BACs from the chromosome 1BS. This data allowed us to study the organization of the wheat gene space along chromosome 1BS. The sequences of the unigenes helped to perform synteny and evolutionary analyses of these unigenes. DNA from MTP clones were pooled into 3D manner: library of MTP clones was stored in 17 plates of 384 wells (24 columns x 16 rows); plate1 pool consist of mixture of DNA from all MTP clones situated in plate 1, Row A pool consist of mixture of DNA from all MTP clones situated in Rows A (from all 17 plates, etc). The set of positive plate, column and row pools for the unigene (represented in microarray) allow to detect the list of putative positive clones (clones from the intersection of positive pools, cleaned using information on physical intersection clones based on clone fingerprints). Hence, all 57 experiments (17 for plate pools, 24 for column pools, and 16 for row pools) have the same experimental factor.
2013-12-06 | E-MTAB-1912 | biostudies-arrayexpress