GEO DataSets

(Submitter supplied) BACKGROUND: Microarray comparative genomic hybridization (CGH) is currently one of the most powerful techniques to measure DNA copy number in large genomes. In humans, microarray CGH is widely used to assess copy number variants in healthy individuals and copy number aberrations associated with various diseases, syndromes and disease susceptibility. In model organisms such as Caenorhabditis elegans (C. more...

Organism:

Caenorhabditis elegans; Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL7085 GPL7084

3 Samples

Download data: PAIR

(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

8 Series

30 Samples

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(Submitter supplied) Oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

2 Series

6 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70/50-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

12 Series

370 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

26 Series

1 Related Platform

672 Samples

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(Submitter supplied) Long oligonucleotides were selected using the program OligoRankPick, described in Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser & Zbynek Bozdech: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinformatics 2007, 8:350. The 70-bp oligonucleotides were spotted onto poly-L-lysine-coated microscopic slides as described in Zbynek Bozdech, Jingchun Zhu, Marcin P Joachimiak, Fred E Cohen, Brian Pulliam & Joseph L DeRisi: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. more...

Organism:

Plasmodium falciparum

3 Series

299 Samples

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(Submitter supplied) Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a “genome proxy” microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. more...

Organism:

uncultured crenarchaeote 4B7; Prochlorococcus marinus subsp. pastoris str. CCMP1986; Prochlorococcus marinus str. MIT 9312; uncultured marine gamma proteobacterium EBAC31A08; uncultured marine bacterium EB0_41B09; uncultured proteobacterium 60D04; Prochlorococcus marinus str. MIT 9313; Prochlorococcus marinus str. MIT 9515; uncultured marine bacterium 577; uncultured gamma proteobacterium eBACHOT4E07; uncultured marine group II euryarchaeote 37F11; uncultured marine bacterium 440; uncultured marine bacterium 583; marine metagenome; uncultured marine alpha proteobacterium; uncultured Pseudomonadota bacterium; uncultured crenarchaeote 74A4; uncultured proteobacterium 65D09; uncultured marine group II euryarchaeote EF100_57A08; uncultured marine bacterium EB000_55B11

Type:

Other

Platform:

GPL6012

28 Samples

Download data: GPR

(Submitter supplied) K14Cre; Brca2F/F; p53F/F tumor analysis Keywords: Comparative Genomic Hybridization, aCGH

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL2851

4 Samples

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(Submitter supplied) Array-based comparative genomic hybridisation is a high-resolution method for measuring chromosomal copy number changes. Here we present a validated protocol using in-house spotted oligonucleotide libraries for array CGH. This oligo array CGH platform yields reproducible results and is capable of detecting single copy gains, multi-copy amplifications as well as homozygous and heterozygous deletions as small as 100 kb with high resolution. more...

Organism:

Homo sapiens; Mus musculus

Type:

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

11 related Platforms

36 Samples

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(Submitter supplied) - clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34) - oncobacs were mapped using their overgo-primers and are available via www.ensembl.org Protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. more...

Organism:

Homo sapiens

2 Series

37 Samples

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(Submitter supplied) hydrophilic polymer containing N-hydroxysuccinimide (NHS) ester reactive groups Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). The oligonucleotides were dissolved at 10 uM concentration in 50 mM sodium phosphate buffer pH 8.5 and single spotted onto CodeLink slides (Amersham Biosciences), using an OmniGrid 100 microarrayer (Genomic Solutions, Ann Arbor, MI, USA) equipped with SMP3 pins (TeleChem International, Sunnyvale, CA, USA). more...

Organism:

Homo sapiens

1 Series

1 Sample

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome - all plates were printed once (no replicate spots) Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys. more...

Organism:

Homo sapiens

1 Series

1 Sample

Download data

(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome - all plates were printed once (no replicate spots) Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Homo sapiens

3 Series

73 Samples

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Compugen to the July 2003 Freeze of the human genome - all plates were printed once (no replicate spots) Protocol: The Human Release 1.0 oligonucleotide library, containing 18861 60-mer oligonucleotides representing 17260 unique genes as designed by Compugen (San Jose, CA, USA) was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Homo sapiens

2 Series

24 Samples

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBIm33 version of the mouse genome - all plates were printed once (no replicate spots) Protocol: The Mouse 8K and Mouse 14K extension oligonucleotide libraries, containing 65-mer oligonucleotides representing 21825 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Mus musculus

2 Series

10 Samples

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(Submitter supplied) - clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34) - oncobacs were mapped using their overgo-primers and are available via www.ensembl.org Protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 5284 clones with known chromosomal positions, was isolated according to the CHORI protocol. more...

Organism:

Homo sapiens

8 Series

160 Samples

Download data

(Submitter supplied) - clones were mapped to the UCSC July 2003 Freeze of the Human Golden Path (NCBI build 34) - oncobacs were mapped using their overgo-primers and are available via www.ensembl.org Protocol: as described in: Carvalho et al (J. Clin. Path.,2004, vol. 57, 644-646). DNA from the 1 Mb resolution Sanger BAC clone set, the OncoBac set, and in house clones of interest, supplemented with clones from the Children’s Hospital Oakland Research Institute (CHORI), amounting to a total of 4678 clones with known chromosomal positions, was isolated according to the CHORI protocol. more...

Organism:

Homo sapiens

4 Series

104 Samples

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome - from a total of 76 384-well plates in the library plates 10 and 11 were printed twice (in duplicate) - all other plates were printed once (no replicate spots) Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Homo sapiens

3 Series

85 Samples

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome - from a total of 76 384-well plates in the library plates 14 and 15 were printed twice (in duplicate) - all other plates were printed once (no replicate spots) Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Homo sapiens

8 Series

51 Samples

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(Submitter supplied) - oligonucleotide sequences are available via www.ensembl.org after agreeing to Compugen's conditions - oligonucleotides were mapped by Ensembl to the NCBI35 version of the human genome - from a total of 76 384-well plates in the library plate 15 was not printed in this platform - all other plates were printed once (no replicate spots) Protocol: The Human Release 2.0 oligonucleotide library, containing 60-mer oligonucleotides representing 28830 unique genes as designed by Compugen (San Jose, CA, USA), was obtained from Sigma-Genosys (Zwijndrecht, The Netherlands). more...

Organism:

Homo sapiens

7 Series

40 Samples

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