GEO DataSets

(Submitter supplied) A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence. The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4130

2 Samples

Download data: TXT

(Submitter supplied) The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7699

2 Samples

Download data: PAIR

(Submitter supplied) We report the application of single-molecule-based sequencing technology for transcription profile analysis of S. cerevisiae strains with different genetic background. By combining the whole genome sequence of these strains, we sought to explore the effects of genome mutations on the transcription diversities.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

3 Samples

Download data: RPKM

(Submitter supplied) Microarray karyotyping (aCGH) of three independent isolates each of four different commerical wine yeast strains was performed. Duplicate arrays (labeled "A" and "B") were performed for each isolate. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platforms:

GPL2634 GPL2633

24 Samples

Download data

(Submitter supplied) CCAAT/enhancer-binding protein alpha (C/EBPα) is a lineage-specific transcription factor that directs development of granulocytes. To obtain insights into the genome-wide transcriptome of wild type C/EBPα, we have performed chromatin immunoprecipitation on DNA promoter microarrays (ChIP-chip) in the murine 32D myeloid progenitor cell line. These cells expressed an estradiol-inducible form of wild-type C/EBPα.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL5811

5 Samples

Download data: CEL, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array; Genome variation profiling by genome tiling array

87 related Platforms

100 Samples

Download data: CEL, CHP, GFF, PAIR, TXT

(Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

60 related Platforms

60 Samples

Download data: GFF, PAIR

(Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

24 related Platforms

24 Samples

Download data: GFF, TXT

(Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL16619

14 Samples

Download data: GFF, TXT

(Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6983

1 Sample

Download data: GFF, TXT

(Submitter supplied) The ideal genome sequence for medical interpretation is complete and diploid, capturing the full spectrum of genetic variation. Toward this end, there has been progress in discovery of single nucleotide polymorphism (SNP) and small (<10bp) insertion/deletions (indels), but annotation of larger structural variation (SV) including copy number variation (CNV) has been less comprehensive, even with available diploid sequence assemblies. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6801

1 Sample

Download data: CEL, CHP, GFF

(Submitter supplied) This array is a Listeria monocytogenes pan-genome tiling array covering the full genomes of 20 L. monocytogenes strains. Each probe on the array may target multiple strains. Each probe may contain either zero or one mismatch to its intended genomic targets. The whole genomes of all 20 strains are tiled at an average depth of coverage of 2.65x, and the 50-mer probes are offset on average 21 bp from one another. more...

Organism:

Listeria monocytogenes; Listeria monocytogenes EGD-e; Listeria monocytogenes serotype 4b str. F2365; Listeria monocytogenes serotype 1/2a str. F6854; Listeria monocytogenes serotype 4b str. H7858; Listeria monocytogenes FSL F2-515; Listeria monocytogenes FSL J1-194; Listeria monocytogenes FSL J1-175; Listeria monocytogenes FSL J1-208; Listeria monocytogenes FSL J2-003; Listeria monocytogenes FSL J2-071; Listeria monocytogenes FSL J2-064; Listeria monocytogenes FSL N1-017; Listeria monocytogenes FSL N3-165; Listeria monocytogenes FSL R2-503; Listeria monocytogenes F6900; Listeria monocytogenes J0161; Listeria monocytogenes J2818; Listeria monocytogenes LO28; Listeria monocytogenes 10403S; Listeria monocytogenes HPB2262

1 Series

18 Samples

Download data: NDF, POS, TXT

(Submitter supplied) Deletions and amplifications of the human genomic sequence (Copy Number Polymorphisms, or 'CNPs') are the cause for numerous diseases and a potential cause of phenotypic variation in the normal population. Comparative Genomic Hybridization (CGH) has been developed as a useful tool for detecting alterations in DNA copy number that involve blocks of DNA several kilobases or greater in size. We have developed High-Resolution CGH (HR-CGH) to detect accurately and with relatively little bias the presence and extent of chromosomal aberrations in human DNA. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL3449 GPL3450 GPL3448

16 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array; Genome variation profiling by genome tiling array

6 related Platforms

375 Samples

Download data: CEL, CHP, PAIR, TXT

(Submitter supplied) Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6433

30 Samples

Download data: TXT

(Submitter supplied) Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7717

60 Samples

Download data: PAIR, TXT

(Submitter supplied) Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4091

60 Samples

Download data: TXT

(Submitter supplied) Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL3718 GPL3720

180 Samples

Download data: CEL, CHP

(Submitter supplied) Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context. We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL6801

45 Samples

Download data: CEL, CHP

(Submitter supplied) Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expression microarray, must first be developed. The aim of the present study was to establish an advanced approach for developing transcriptomics resources for non-model organisms by combining next-generation sequencing (NGS) and microarray technology. more...

Organism:

Chironomus riparius; Anopheles gambiae

Type:

Genome variation profiling by array

Platform:

GPL18083

2 Samples

Download data: TXT