Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mixing Experiment - Mouse Kidney and Spleen

ABSTRACT: 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.

ORGANISM(S): Mus musculus

SUBMITTER: Steven Head

PROVIDER: E-GEOD-27587 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

DNA methylation titration data from two samples with known methylation differences

2010-12-01 | GSE23789 | GEO

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

2005-10-28 | GSE3508 | GEO

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.

2011-03-02 | GSE27587 | GEO

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

MOE430 whole mouse - mouse colon dilution series - RMA preprocessed

2005-06-30 | GSE2850 | GEO

Label free nano-LC MALDI-TOF-MS/MS analysis of Triton X-100 solubilized proteins from bovine brain capillary endothelial cells (BCECs).

Project description:Triton X-100 soluble crude extract from BCECs displaying limited blood-brain barrier functions was fractionated into 5 fractions (F0, F25, F50, F75) with increasing concentrations of acetonitrile (0%, 25%, 50%, 75%). This is the merging of triplicate dataset of subfraction # F0.

2012-11-27 | PRD000681 | Pride

Calibration data mammalian array: Human, Mouse, Rat

Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from synthetic DNA from 3 species. The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement from a given species. The mammalian array was applied to synthetic DNA data from 3 species: human (n=10 mammalian arrays, 2 per methylation level), mouse (n=20, 4 per methylation level), and rat (n=15, 3 per methylation level).

2021-08-27 | GSE174567 | GEO

Transcription profiling of whole adult mouse and adult mouse colon in different dilutions analysed in multiple centers

Project description:This data is part of a large-scale platform comparison experiment. Whole mouse and adult mouse colon RNA was mixed at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100) and distributed across multiple centers for analysis. Eight microarray platforms and RT-PCR were tested for different labeling protocols, amplification protocols, and data preprocessing approaches in order to maximize data intercomparability. The role of universal reference RNA was also examined. Probes of different platforms were matched using gene symbols and/or RefSeq/GenBank accession numbers. Several different normalization procedures were applied. Evaluation criteria included linearity, sensitivity/specificity, and reproducibility within and between platforms, labeling methods, and laboratories. Experiment Overall Design: Whole mouse (sacrificed on day 1, strain: C57BL/6) and adult mouse (8 weeks, strain: C57BL/6 ) colon RNA from multiple animals was pooled respectively. RNA was purified following the manufacturerâs recommendations and integrity was analyzed using an Agilent BioAnalyzer 2100 according to manufacturer instructions. Five RNA samples were created by mixing the two original samples at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100). The five master mix samples were then divided into duplicate sets of the five sample RNAs, distributed to individual laboratories, and hybridized to eight different microarray platforms at several different genome centers. The five samples included here were prepared from 10ng of total RNA using a T7 double amplification protocol as described in Schwab et al., 2003 and hybridized to Affymetrix MOE430 arrays as recommended by the manufacturer using the standard protocol. No replicates were produced.

2008-06-12 | E-GEOD-2850 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data