Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA

ABSTRACT: RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

ORGANISM(S): Mus musculus

PROVIDER: GSE3974 | GEO | 2006/01/05

SECONDARY ACCESSION(S): PRJNA104879

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Contribution of unique genes by individual cell lines to Universal Human Reference RNA

Project description:Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

2006-01-05 | GSE3972 | GEO

Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA

Project description:RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Computed

2006-01-04 | E-GEOD-3974 | biostudies-arrayexpress

Transcription profiling of 10 individual human cell lines to identify unique genes contributed by individual cell lines to UHRR

2005-11-01 | E-SMDB-2653 | biostudies-arrayexpress

Array CGH after human challenge

Project description:Array CGH of H. pylori strain BCS100 after challenge to a new host (patients and experiment described in Graham et al., 2004, Gut, 53:1235-1243). Genomic DNA (500 ng) from the ouput from singel colony isolates obtained 15 or 90 days post innoculation were labeled with Cy5 (red) and cohybridized with 500 ng of genomic DNA from the innoculating strain BCS100 labeled with Cy3 (green). A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design

2007-08-09 | GSE7619 | GEO

Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls

Project description:Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

2006-01-05 | GSE3973 | GEO

Expression Analysis of Gastric Cancers

Project description:Microarray Expression profiles from 58 samples comprising of 3 normals and 55 gastric cancers is used for molecular subclassification of Gastric Cancers. Data Generation and Processing: The ratiometric data here is given by Ch1(Cy3)/Ch2(Cy5) where Ch2 is Universal Reference RNA from Stratagene. Two different chips were used (13K and 18k); The ratio metric is given by (Biological sample / Universal Reference). The Biological Samples are labeled with Cy3 (Green) and the Universal Reference RNA is always labeled with Cy5 (Red). Two types of spots were excluded a) Spots for which Foreground intensity was lower from background by lesser than 10 fluoresence units. b) Spots that couldnt be identified reliably by the scanner (Arrayworx) software within the "region of interest" masked by the user. The 2 channels for each array are equalized by multiplying the reference channel Ch2(Cy5) by a constant which is derived by (Total Cy3 / Total Cy5). Subsequently, all expression ratios from each array is normalized to have median expression value = 1. Keywords: other

2005-07-25 | GSE2637 | GEO

Transcription profiling of 10 individual human cell lines to identify unique genes contributed by individual cell lines to UHRR

2005-11-01 | E-SMDB-2651 | biostudies-arrayexpress

Normal blood cell subtypes

Project description:We used antibodies coupled to magnetic beads (MACS) to purify cell types out of whole blood from healthy donors (CD4+ T cells, CD8+ T cells, and B cells). We also profiled whole blood (collected in Pax tubes) and Peripheral Blood Mononuclear cells obtained by Ficoll-Paque based separation. RNA was extracted using Trizol, amplified linearly twice, labeled with Cy5 and co-hybridized with amplified Stratagene human reference (labeled with Cy3). A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design

2006-05-23 | GSE4889 | GEO

Peripheral blood lymphocytes: ALS patients vs. healthy controls

Project description:Transcripional profiling of lymphocytes from patients with amyotrophic lateral sclerosis (ALS) (n=11) and healthy control subjects (n=11). The goal was to determine disease response expression signatures relevant of ALS pathogenesis that affect brain and spinal cord. The reference design was used: each Cy5-labeled cRNA sample from ALS patient or healthy control subject was cohybridized on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F with the reference pool formed with equal amounts of Cy3-labeled cRNAs from each sample from the healthy control group.

2011-12-11 | GSE28253 | GEO

Human Cells Time of Replication (ToR)

Project description:Measurment of the ToR by comapring the DNA content of the S phase and the DNA content of the G1 phase, the method is based on the method used in the paper - Replication timing of the human genome by Woodfine et al. that was published in Hum. Mol. Genet. 2004. Briefly, after staining with Propidium Iodide, cells in G1 and S phase of the cell cycle are sorted by FACS sorter (ARIA or Vantage), DNA is then extracted from the fractions and differentially labeled with dUTP-Cy3 or dUTP-Cy5 using direct labeling (Agilent labeling kit). The labeled DNA is cohybridized to the array. Early replicating sequences correspond to the spots with high S/G1 ratio and late replicating sequences correspond to the spots with low S/G1 ratio.

2010-05-25 | GSE17235 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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