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Maskless photolithography genome tiling experiment

ABSTRACT: This experiment was designed to identify transcribed sequences across the human genome, particularly those distinct from previously annotated genes. To measure global transcriptional activity a series of high-density oligonucleotide tiling arrays was constructed to represent sense and antisense strands of the entire nonrepetitive sequence of the genome (1.5 Gb). A total of 51,874,388 36mer oligonucleotide probes, positioned every 46 nt on average, were synthesized via maskless photolithography at a feature density of approximately 390,000 probes per slide. The arrays were hybridized to fluorescence-labeled cDNA reverse-transcribed from triple-selected poly (A)+ liver tissue RNA. Keywords = transcription Keywords = gene expression Keywords = human Keywords: other

ORGANISM(S): Homo sapiens

PROVIDER: GSE1904 | GEO | 2004/10/29

SECONDARY ACCESSION(S): PRJNA90967

REPOSITORIES: GEO

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Maskless photolithography genome tiling experiment

Project description:This experiment was designed to identify transcribed sequences across the human genome, particularly those distinct from previously annotated genes. To measure global transcriptional activity a series of high-density oligonucleotide tiling arrays was constructed to represent sense and antisense strands of the entire nonrepetitive sequence of the genome (1.5 Gb). A total of 51,874,388 36mer oligonucleotide probes, positioned every 46 nt on average, were synthesized via maskless photolithography at a feature density of approximately 390,000 probes per slide. The arrays were hybridized to fluorescence-labeled cDNA reverse-transcribed from triple-selected poly (A)+ liver tissue RNA. Keywords = transcription Keywords = gene expression Keywords = human

2004-10-29 | E-GEOD-1904 | biostudies-arrayexpress

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Project description:This experiment was designed to identify transcribed regions of japonica subspecies of the rice genome. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of all the 12 chromosomes were designed to measure genome-wide transcription. A total of 12253842 36mer oligonucleotide probes positioned every 46 nt on average were used for this purpose. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA population (seedling root, seedling shoot, panicle, and suspension cultured cells). Keywords: tiling array, genome-wide transcription

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Tiling microarray analysis of japonica and indica rice chromosome 10

Project description:This experiment was designed to identify transcribed regions of both japonica and indica rice chromosome 10. A series of high-density oligonucleotide tiling arrays that represent sense and antisense strands of the entire nonrepetitive sequence of the chromosome were used to measure transcriptional activities. A total of 750,282 and 838,816 36mer oligonucleotide probes, positioned every 46 nt on average, were designed to interrogating the japonica and the indica chromosome, respectively. The probes were synthesized via maskless photolithography at a feature density of approximately 389,000 probes per slide. The arrays were hybridized with fluorescence-labeled cDNA reverse-transcribed from equal amounts of four selected poly(A)+ RNA populations, namely, seedling roots, seedling shoots, panicles, and suspension cultured cells of the respective rice subspecies. Keywords: other

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ENCODE ChIP-chip for STAT1 on Human Hela S3 Cells

Project description:STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays. Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays Keywords: other

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Transcriptional Profile of Lactobacillus helveticus grown in milk vs. MRS medium

Project description:L. helveticus is used to modulate cheese flavor and as a starter organism in certain cheese varieties. Our group has compiled a draft (4x) sequence for the 2.4 Mb genome of an industrial strain L. helveticus CNRZ32. The primary aim was to investigate expression of 168 completely sequenced genes during growth in milk and MRS medium using microarrays. Oligonucleotide probes against each of the completely sequenced genes were compiled on maskless photolithography-based DNA microarrays. Additionally, the entire draft genome sequence was used to produce tiled microarrays where the non-interrupted sequence contigs were covered by consecutive 24-mer probes. Keywords: growth conditions response

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Homo sapiens

Project description:Maskless photolithography genome tiling experiment

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Transcriptional Analysis of 1M Regions in Glycine max Using Tiling Microarrays

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2010-05-26 | E-GEOD-10056 | biostudies-arrayexpress

Transcriptional Analysis of 1M Regions in Medicago truncatula Using Tiling Microarrays

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