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Transcription profiling of human neuroblastoma sample to investigate the differences between Agilent long oligonucleotide arrays verse Affymetrix short oligonucleotide arrays -IMR32 cells

ABSTRACT: Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to measure differential gene expression in RNA samples generated from human neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10ÂµM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11865, 11866, 11858, 11857, 11870, and 11871) which represent the RNA preps harvested at three different time (April 17, 2001, March 15, 2001, and Feb 21, 2001). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The RNA prep used for Agilent array analysis was not the same as the one used for Affymetrix array analysis. Finally, three replicates (GSM 11828, 11831 and 11835) were generated.

ORGANISM(S): Homo sapiens

SUBMITTER: Jiang Li

PROVIDER: E-GEOD-761 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Long oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cells

Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to measure differential gene expression in RNA samples generated from human neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11865, 11866, 11858, 11857, 11870, and 11871) which represent the RNA preps harvested at three different time (April 17, 2001, March 15, 2001, and Feb 21, 2001). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The RNA prep used for Agilent array analysis was not the same as the one used for Affymetrix array analysis. Finally, three replicates (GSM 11828, 11831 and 11835) were generated. Keywords: parallel sample

2003-10-22 | GSE761 | GEO

Long oligonucleotide arrays verse short oligonucleotide arrays-CTX066

Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11755, 11756, 11780, 11781, 11782, and 11783) which represent the RNA preps harvested at three different time (Jan 16, 2002, Jan 24, 2002, and Feb 20, 2002). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The same RNA preps used for Affymetrix array analysis were also used for Agilent array analysis. Finally, three replicates (GSM 11803, 11804 and 11809) were generated. Keywords: parallel sample

2003-10-22 | GSE759 | GEO

Transcription profiling of human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20A?M) for 24h and assayed with long oligonucleotide arrays verse short oligonucleotide arrays-CTX066

Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20ÂµM) for 24h. For Affymetrix technology, RNAs from vehicle or tBHQ treated groups were analyzed separately. There are three replicates (GSM 11755, 11756, 11780, 11781, 11782, and 11783) which represent the RNA preps harvested at three different time (Jan 16, 2002, Jan 24, 2002, and Feb 20, 2002). For Agilent arrays, amplified cRNAs generated from vehicle or tBHQ treated groups were labeled with cy3 or cy5 and were competitively hybridized with Hu 1A oligo arrays. The same RNA preps used for Affymetrix array analysis were also used for Agilent array analysis. Finally, three replicates (GSM 11803, 11804 and 11809) were generated.

2008-06-15 | E-GEOD-759 | biostudies-arrayexpress

Neural stem and neuroblastoma cells

2003-10-22 | GSE768 | GEO

Transcription profiling of human neural stem and neuroblastoma cells

Project description:Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from (1) human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20ÂµM) for 24h, and (2) neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10ÂµM) for 24h. This SuperSeries is composed of the following subset Series:; GSE759: Long oligonucleotide arrays verse short oligonucleotide arrays-CTX066; GSE761: Long oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cells Experiment Overall Design: Refer to individual Series

2008-06-15 | E-GEOD-768 | biostudies-arrayexpress

Spotted long oligonucleotide arrays

Project description:Both spotted long oligonucleotide arrays and Affymetrix GeneChips were used to measure differential gene expression in two RNA samples (K562 erythroleukemia RNA and the Stratagene Universal Human Reference RNA). For Affymetrix technology, the two RNAs were analyzed separately. There are two replicates for K562 RNA (GSM4843 and GSM4844) and three for the Stratagene Universal reference (GSM4845-GSM4847). Two types of spotted long oligonucleotide arrays were used. These arrays were used to do two-color hybridizations to directly compare K562 and Universal reference RNAs. One array (GPL273) was made with probes from the Operon Human Genome Oligo Set Version 1. These arrays were used with unamplified cDNA probes (6 replicates, GSM4848-GSM4853), with aRNA probes produced by one round of T7 RNA polymerase-based amplification (6 replicates, GSM4854-GSM4859), and with aRNA probes produced by two rounds of amplification (2 replicates, GSM4860-GSM4861). Keywords: parallel sample

2003-03-18 | GSE344 | GEO

Nrf2 Knockout vs. Wildtype mice, liver sample

Project description:In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the liver of Nrf2 knockout and wildtype mice at 5 month age. Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13431, 13435) for the female Nrf2 wildtype group, two replicates (GSM 13439, 13441) for the male Nrf2 wildtype group, two replicates (GSM 13436, 13437) for the female Nrf2 knockout group, and two replicates (GSM 13438, 13440) for the male Nrf2 knockout group. Keywords: parallel sample

2003-12-16 | GSE864 | GEO

Nrf2 Knockout vs. Wildtype mice, spleen sample

Project description:In situ synthesized oligo arrays, U74Av2, from Affymetrix were used to measure differential gene expression in RNA samples generated from the spleen of Nrf2 knockout and wildtype female mice at 5 month age. Total RNAs from two Nrf2 knockout or wildtype littermates were analyzed separately. There are two replicates (GSM 13470, 13472) for the female Nrf2 wildtype group and two replicates (GSM 13467, 13469) for the female Nrf2 knockout group. Keywords: parallel sample

2003-12-16 | GSE865 | GEO

Oligonucleotide-based arrayCGH

Project description: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. A human oligonucleotide library was printed on amine binding slides. Arrays were hybridised using a hybstation and analysed using BleuFuse feature extraction software, with over 95% of spots passing quality control. The protocol allows as little as 300 ng of input DNA without the need for amplification or target reduction and a 90% reduction of Cot1-DNA without compromising quality. High quality results have also been obtained with DNA from archival tissue. Finally, in addition to human oligo arrays, we have applied the protocol successfully to mouse oligo arrays. We believe that this oligo-based platform using “off-the-shelf” oligo-libraries provides an easy accessible alternative to BAC arrays for CGH, which is cost-effective, available at high resolution and easily implemented for any sequenced organism without compromising the quality of the results. Keywords: comparative genomic hybridization, oligonucleotide,

2005-12-19 | GSE3264 | GEO

PD991 Gene Expression Arrays

Project description:Agilent gene expression arrays were used for intrinsic subtyping and to measure changes after anastrozole (C1D1) and after combination of anastrazole and palbociclib (C1D15).

2017-04-07 | GSE93204 | GEO

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