GEO DataSets

(Submitter supplied) Isolated deletions of the long arm of chromosome 5 (del(5q)) are observed in 10% of myelodysplastic syndromes (MDS) and are associated with a more favorable prognosis, although the clinical course varies considerably. If one or more additional chromosomal aberration/s are present this correlates with a significant shorter overall survival. To assess the frequency of hidden abnormalities in cases with an isolated cytogenetic del(5q), we have performed a genome wide high resolution 44K 60mer oligonucleotide array CGH study using DNA from bone marrow cells of 12 MDS and one AML patient. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL2873 GPL2879

13 Samples

Download data: TXT

(Submitter supplied) Myelodysplastic syndromes (MDS) are a group of clonal disorders of hematopoietic stem cells. Mesenchymal stem cells (MSC) are the progenitors of the Bone Marrow (BM) stroma and have been involved in the physiopathology of MDS. The presence of cytogenetic aberrations on MSC from MDS patients is controversial. The aim of the study is to characterize BM derived MSC from patients with MDS using: kinetic studies, immunophenotyping, fluorescent in situ hybridisation (FISH) analysis and genetic changes by array based comparative genomic hybridization (array-CGH). more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL6575

13 Samples

Download data: GPR

(Submitter supplied) AML/MDS patients carrying 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are characterized by a later onset, a complex aberrant karyotype (CAK) frequently including deletions within 5q, 17p and 7q, as well as fast progression of the disease with extremely poor prognosis. We and other have shown that the MLL gene is over expressed in amplified cases, however, in most of the cases the amplified region is not restricted to the MLL locus. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

15 Samples

Download data: CEL

(Submitter supplied) AML/MDS patients carrying 11q amplifications involving the mixed lineage leukemia gene (MLL) locus are characterized by a complex aberrant karyotype (CAK) frequently including deletions within 5q, 17p and 7q, a later onset and fast progression of the disease with extremely poor prognosis. We and others have shown that the MLL gene is overexpressed in amplified cases; however, in most of the cases the amplified region is not restricted to the MLL locus. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL5000

12 Samples

Download data: GPR

(Submitter supplied) Lenalidome is a drug especially effective in low risk myelodysplastic syndromes (MDS) with isolated 5q deletion. However, 25% of the patients did not respond. TP53 mutations have been described to play a role in the disease progression, and karyotypic complexity also has an important impact in the outcome. We selected 53 MDS patients with 5q deletion and treated with lenalidomide and we studied by the following techniques: conventional G-banding cytogenetics (CC), single nucleotide polymorphism arrays (SNP-A) and sequencing, in order to assess their impact on treatment response and disease progression. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL3718 GPL6801

81 Samples

Download data: CEL, CNCHP, LOHCHP

(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

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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 (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

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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

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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(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 12 and 13 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

37 Samples

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(Submitter supplied) PURPOSE: Bone marrow (BM) is a common homing organ for early disseminated tumor cells (DTC) and their presence can predict the subsequent occurrence of overt metastasis and survival in lung cancer. It is still unclear whether the shedding of DTC from the primary tumor is a random process or a selective release driven by a specific genomic pattern. EXPERIMENTAL DESIGN: DTCs were identified in BM from lung cancer patients by an immunocytochemical cytokeratin assay. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platforms:

GPL3055 GPL2819

30 Samples

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