Pooled potato BAC clones
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Project description:A synthetic autopolyploidy plant series O37 was developed from chromosome doublings of a monoploid (12 chromosome) plant derived from a Solanum phureja background. Monoploid (1x), diploid (2xR3 and 2xR5) and tetraploid (4x) plants were used for gene expression profiling. Total RNA was isolated from growing leaflets of six plants of each genotype at 20 day after planting. Total RNA was isolated and amplified from growing root tips of each genotype at 7 days after planting. Keywords: Genotype, Tissue type, Biorep, Loop design
2006-08-02 | GSE5428 | GEO
Project description:A synthetic autopolyploidy plant series O37 was developed from chromosome doublings of a monoploid (12 chromosome) plant derived from a Solanum phureja background. Monoploid (1x), diploid (2xR3 and 2xR5) and tetraploid (4x) plants were used for gene expression profiling. Total RNA was isolated from growing leaflets of six plants of each genotype at 20 day after planting. Total RNA was isolated and amplified from growing root tips of each genotype at 7 days after planting. Microarray hybridizations were performed in a loop design for three biological replicates.
2010-07-01 | E-GEOD-5428 | biostudies-arrayexpress
Project description:High resolution BAC array used to study changes in the copy number of chromosome 21 in Acute Meyloid Leukemia patients Genomic DNA from patients as well as from normal donors were differentially labelled and hybridized on the array 36 RPCI-11 BAC clones covering the q-arm of chromosome21 from position15.1MB(close to the centromere)to the telomeric position 46.9 MB with an average gap between clones of 800 kb (range 346-1593 kb)In addition 23 randomly selected clones, each representing 1 of the remaining chromosomes1-20,22,X and YPositions of genes and BAC clones were determined according to the NCBI (http://www.ncbi.nlm.nih.gov/mapview) 59 BAC clones spotted in 6 replicas for a total 354 spots on GAPII corning glass slides using Affymetrix GMS417 Affymetrix Arrayer with 4-ring&pin configuration. (Affymetrix,Santa Clara, CA). Purified clones spotted in 50%DMSO DNA Isolation of these clones was performed from bacterial culture (250ml) using Qiagen midi kit (Qiagen, Valencia CA) gDNA from AML patients and healthy controls was extracted and labelleb according to the published protocol by JR Pollack in Nature Genetics vol.23 Sep.99, also available http://cmgm.stanford.edu/pbrown/protocols/4_genomic.html Fluorescence intensity ratios were measured in control experiments (reference versus reference hybridization) to weight DNA Amplification or deletion Fluorescence ratio >1 indicates amplification, Fluorescence ratio <1 indicate deletion Mean of the background corrected pixel-by-pixel fluorescence ratio between the two dyes at each spot was obtained by genePix software. Series_platform_id: my_array13 Series_submitter weblink: www.dnaarrays.org Keywords: other
2004-02-29 | GSE1078 | GEO
Project description:Hybridization using overgo probes is an established approach for screening arrayed bacterial artificial chromosome (BAC) libraries. We have improved the use of overgos by increasing the yield of positive clones using reduced levels of radioisotopes and enzyme. The strategy involves labeling with all four radiolabeled nucleotides in a hot pulse followed by a cold nucleotide chase and then extending the exposure time to compensate for reduced specific activity of the probes. The resulting cost savings and reduced human exposure to radiation make the use of highly pooled overgo probes a more attractive approach for screening of BAC libraries from organisms with large genomes.
| S-EPMC1761434 | biostudies-literature
Project description:High resolution BAC array used to study changes in the copy number of chromosome 21 in Acute Meyloid Leukemia patients Genomic DNA from patients as well as from normal donors were differentially labelled and hybridized on the array 36 RPCI-11 BAC clones covering the q-arm of chromosome21 from position15.1MB(close to the centromere)to the telomeric position 46.9 MB with an average gap between clones of 800 kb (range 346-1593 kb)In addition 23 randomly selected clones, each representing 1 of the remaining chromosomes1-20,22,X and YPositions of genes and BAC clones were determined according to the NCBI (http://www.ncbi.nlm.nih.gov/mapview) 59 BAC clones spotted in 6 replicas for a total 354 spots on GAPII corning glass slides using Affymetrix GMS417 Affymetrix Arrayer with 4-ring&pin configuration. (Affymetrix,Santa Clara, CA). Purified clones spotted in 50%DMSO DNA Isolation of these clones was performed from bacterial culture (250ml) using Qiagen midi kit (Qiagen, Valencia CA) gDNA from AML patients and healthy controls was extracted and labelleb according to the published protocol by JR Pollack in Nature Genetics vol.23 Sep.99, also available http://cmgm.stanford.edu/pbrown/protocols/4_genomic.html Fluorescence intensity ratios were measured in control experiments (reference versus reference hybridization) to weight DNA Amplification or deletion Fluorescence ratio >1 indicates amplification, Fluorescence ratio <1 indicate deletion Mean of the background corrected pixel-by-pixel fluorescence ratio between the two dyes at each spot was obtained by genePix software. Series_platform_id: my_array13 Series_submitter weblink: www.dnaarrays.org
2010-06-09 | E-GEOD-1078 | biostudies-arrayexpress
Project description:BackgroundGenome sequencing of barley has been delayed due to its large genome size (ca. 5,000 Mbp). Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H.ResultsWe sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1.ConclusionsWe demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.
| S-EPMC3224129 | biostudies-literature
Project description:To obtain further insights into the role of bacterial activity in BAC filter performance, the expressed proteins of the bacterial community residing in the BAC filter were identified by a metaproteomic approach.
2022-10-13 | PXD015811 | Pride
Project description:The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. The discovery and characterization of the proteins mediating this host–pathogen interaction enable the understanding of the pathosystem and is the key for developing resistant plants. Keywords: SAGE-Solexa, inoculation response, transcript profiling, Solanum phureja, Phytophthora infestans Four-week-old yellow potato (Solanum phureja) plants were inoculated with Phytophthora infestans and were collected and flash frozen in liquid nitrogen at 12 and 72 hours post inoculation, as well as mock inoculated, for RNA extraction. 2 yellow potato cultivars (resistant and susceptible) were used for each experiment. Mock inoculated plants were collected in each replicate. RNA obtained from each of the three biological replicates was pooled to obtain a single RNA sample for each timepoint X cultivar combination. A total of 6 different SAGE libraries were thus obtained. For all libraries, Illumina sequencing was performed at Canada´s Michael Smith Genome Sciences Centre.
2009-06-13 | E-GEOD-11781 | biostudies-arrayexpress
Project description:P. aeruginosa is the leading cause of death in patients with cystic fibrosis patients and one of the most problematic bacterial pathogens responsible for hospital-acquired infections. This pathogen has a high capacity to form biofilms on inert and living surfaces. This lifestyle allows it to persist in various hospital niches or on medical device which become vectors of contamination. Chronic infections are extremely complicated to eradicate due to the remarkable antimicrobial resistance of biofilms leading to a persistence in the tissue and an immune system exhaustion. It is therefore becoming essential to understand the mechanisms of biofilm formation to find new therapeutic targets in order to develop effective antibiofilm strategies. We previously identified in P. aeruginosa PA01 biofilms an accumulation of a hypothetical protein named PA3731 and its deletion impacted the biofilm formation. Similarly, to PspA, a protein from the well-known Psp system of E. coli, PA3731 is a has a predicted structure mostly helical, a PspA/IM30 domain and was accumulated during an osmotic shock. In P. aeruginosa genome, PA3731 appears to form a cluster with 3 genes (PA3732 to PA3729) that we named BAC system for “Biofilm Associated Cluster”. Here we worked on the PA14 strain and focus our study on PA14_16140, the PA3732 homologue. Using a ∆16140 mutant and phenotypic approach, we confirmed the role of the BAC system in the virulence and biofilm formation. We added supplementary genes coding the BAC system and demonstrate that altogether they form an operonic structure regulates by RpoN. We get further insight the role PA14_16140 by proteomic quantitative approach revealing an accumulation of the BAC system proteins in ∆16140 biofilms suggesting its regulatory role of the bac operon. Moreover, we present here the first crystallographic structure of PA14_16140. To summarise, according to our studies, and although further analysis is still required, this newly discovered operon appears composed firstly of its regulator and then of a homologous PspA.
2024-02-15 | PXD044736 | Pride
Project description:The late blight pathogen, Phytophthora infestans has a broad host range within the Solanaceae family, including yellow potato (Solanum phureja). The disease caused by P. infestans in S. phureja is poorly understood and is a major concern in Colombia. Expressed Sequence Tag (EST) libraries obtained from a normalized library constructed from healthy plant tissue revealed high levels of sequence similarity between S. phureja and S. tuberosum. Then, utilizing Serial Analysis of Gene Expression and high-throughput sequencing (SAGE-Solexa), we characterized yellow potato gene expression during infection by P. infestans. Four-week-old yellow potato plants were inoculated with P. infestans and were collected at 12 and 72 hours post inoculation for RNA extraction. We detected differentially expressed genes by comparing inoculated to non-inoculated and resistant to susceptible plants. The discovery and characterization of the proteins mediating this host–pathogen interaction enable the understanding of the pathosystem and is the key for developing resistant plants. Keywords: SAGE-Solexa, inoculation response, transcript profiling, Solanum phureja, Phytophthora infestans
2009-06-13 | GSE11781 | GEO