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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (22k Linearity)

ABSTRACT: E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design

ORGANISM(S): Mus musculus

PROVIDER: GSE3508 | GEO | 2005/10/28

SECONDARY ACCESSION(S): PRJNA93547

REPOSITORIES: GEO

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Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (22k Linearity)

Project description:E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design E12.5 mouse whole embryo and E12.5 placenta total RNA were pooled to create 25:75, 50:50, and 75:25 ratio mixtures, based on Bioanalyzer quantitation. These samples, along with the original unmixed RNAs, were used as templates for duplicate linear amplification labeling reactions. cRNA target mixtures were hybridized against a Universal Mouse Reference (Stratagene). Pairwise comparison using the NIA Microarray Analysis (ANOVA) software produced log ratios, which were compared to the expected log ratios for genes showing statistically significant (FDR<0.05) differential expression between unmixed embryo and placenta.

2010-06-09 | E-GEOD-3508 | biostudies-arrayexpress

Transcription profiling of E12.5 mouse whole embryo and E12.5 placenta total RNA pooled to create 25:75, 50:50, and 75:25 ratio mixtures to estimate transcript copy number

2005-01-01 | E-MNIA-67 | biostudies-arrayexpress

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)

2005-10-28 | GSE3509 | GEO

Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray (WGA 2.1 Spike Test)

Project description:E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance. Keywords: cell type comparison design,development or differentiation design,normalization testing design,reference design E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells were compared on a novel microarray design to validate the system. The in situ-synthesized 60-mer oligonucleotide microarray platform contains approximately 44,000 DNA features, and was designed to detect transcripts from all known genes, as well as about 5,000 potential genes, as identified by the NIA Mouse Gene Index 2.0. Seven external RNA controls were derived from intronic and intergenic yeast genome sequences, and 60-mer probes were spotted 10 time each on the slides. These spike-in RNA controls were diluted to cover 7 orders of magnitude in initial concentration, and used to define a function relating signal intensity to transcript abundance.

2005-10-28 | E-GEOD-3509 | biostudies-arrayexpress

Mixing Experiment - Mouse Kidney and Spleen

Project description:The design of this experiment was based on the assumption that transcript levels will change linearly while going from 100 percent of one tissue to 100 percent of the other. This assumed linear data set could be used to evaluate various issues related to low-level microarray data analysis. Hybridization cocktails from two mouse tissues, kidney and spleen, were prepared and mixed in a range of ratios and applied to 4-5 replicate GLYCOv1 chips for analysis. The mixture ratios were as follows: 100 percent kidney, 75 percent Kidney/25 percent spleen, 50 percent kidney/50 percent spleen, 25 percent kidney/75 percent spleen, and 100 percent spleen.

2011-03-02 | E-GEOD-27587 | biostudies-arrayexpress

Temporal bovine liver gene expression

Project description:Liver from five Holstein cows fed to current National Research Council (2001) recommendations during the dry period and early lactation was biopsied at -65, -30, -14, 1, 14, 28, and 49 days relative to parturition. cDNA from liver and a reference standard (made from cattle tissues not including liver or mammary) were labeled with Cy3 or Cy5 fluorescent dye and co-hybridized to our 7,872 bovine cDNA microarray using a dye-swap design. More than 5,000 sequences present on the array were expressed in liver. Normalized log-transformed ratios (liver/reference) were analyzed using a MIXED model in SAS. Keywords: cow, liver, lactation, microarray, periparturient period Keywords: time-course

2005-08-10 | GSE2692 | GEO

Transcription profiling of E12.5 mouse whole embryo, E12.5 placenta, embryonic stem (ES) cells, and trophoblast stem (TS) cells on a novel microarray design to validate the system

2005-01-01 | E-MNIA-66 | biostudies-arrayexpress

Sulfolobus solfataricus P2 growth curve, tiling arrays

Project description:Experimentally mapped transcriptome structure of Sulfolobus solfataricus P2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 25 nt). Sulfolobus solfataricus P2 growth curve experiments were conducted in batch culture. Reference samples were cultured at mid-log phase (OD600 = 0.312). Eight samples were collected that spanned the key phases of the growth curve. Total RNA from samples of growth curve and reference were directly labeled with Cy3 or Cy5, and were hybridized to the tiling array. Dye-flip experiments were done for each sample. Log ratios were calculated for each probe (growth curve sample/reference). Transcriptome browser is available at http://baliga.systemsbiology.net/enigma/.

2011-06-27 | E-GEOD-26779 | biostudies-arrayexpress

An experimental loop design improves the detection of congenital chromosomal aberrations by array CGH

Project description:Comparative genomic hybridization microarrays (array CGH or molecular karyotyping) for the detection of congenital chromosomal aberrations is the application of microarray technology that is coming fastest into routine clinical application. When using a two-channel microarray of genomic DNA probes for array CGH, the basic setup consists in hybridizing a patient sample against a normal reference sample and detecting copy number variations through the deviation of fluorescent signal intensity between patient and normal reference. Two major disadvantages of this setup are (1) the use of half of the resources to measure a (little informative) reference sample and (2) the possibility that deviating signals are caused by benign copy number variation in the “normal” reference instead of a patient aberration. We therefore propose a new experimental loop design that compares three patients in three hybridizations (Patient 1 vs. Patient 3, Patient 3 vs. Patient 2, and Patient 2 vs. Patient 1). We develop and compare two statistical methods (linear models of log ratios and mixed models of absolute measurements). In an analysis of data from 27 patients seen at our genetics center, this new setup together with the linear model analysis significantly overcomes the limitations of the classical setup. Furthermore, we observed that the linear models of the log-ratios had a higher signal-to-noise ratio than the mixed models of the absolute intensities. These improvements are important to guarantee a maximal efficiency of array CGH in a clinical setting and will therefore contribute to its quick adoption as a routine diagnostic tool. The method is implemented as a web application and is available at www.esat.kuleuven.be/loop. Keywords: comparative genomic hybridization

2007-12-01 | GSE6538 | GEO

DNA methylation titration data from two samples with known methylation differences

Project description:Two samples with known methylation differences. Sample A is NA 10923 from Coriell Institute for Medical Research. It is a B-Lymphocyte sample from a male donor. Sample B is HTB-38 cell line from ATCC (http://www.atcc.org). It is a colon cancer sample from a female donor. Sample A and B were normalized into the same concentration, and then mixed in five different titration ratios: 100:0, 90:10, 75:25, 50:50 and 0:100 Sample A and Sample B were mixed in five different titration ratios: 100:0, 90:10, 75:25, 50:50 and 0:100

2010-12-01 | E-GEOD-23789 | biostudies-arrayexpress

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