Wilms tumor versus Stratagene Universal Reference
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE1158 | GEO | 2004/12/31
SECONDARY ACCESSION(S): PRJNA87293
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression comparison of Wilms tumor RNA versus Stratagene Universal reference RNA
2008-06-11 | E-GEOD-1158 | biostudies-arrayexpress
Project description:Wilms tumor versus Stratagene Universal Reference
| PRJNA87293 | ENA
Project description:In present study we optimized and validated the mDOT-seq approach with miRXplore Universal Reference (Miltenyi Biotec) RNA. The results revealed that the 3' adapters with alkyne moieties attached to the fifth carbon atom of the second cytosine or uracil in ACTC and CUCC sequences, respectively, are best suited for the preparation of RNA sequencing libraries.
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Project description:Stratagene universal human RNA hybridized to both U133 Plus 2.0 and U133 A arrays. Keywords: Affymetrix platform comparison
2006-07-25 | GSE3061 | GEO
Project description:UMRR (Universal Mouse Reference RNA, Catalog #740100) was purchased from Stratagene and used as the starting material. Liver total RNA (Catalog #64042-1) was purchased from Clontech and used as the starting material. UMRR was labeled with Cyanine-3 (Green) while Liver was labeled with Cyanine-5 (Red). cRNA was made by the single round amplification method. Keywords: repeat sample
2003-03-07 | GSE333 | GEO
Project description:UMRR (Universal Mouse Reference RNA, Catalog #740100) was purchased from Stratagene and used as the starting material. Spleen total RNA (Catalog #64044-1) was purchased from Clontech and used as the starting material. UMRR was labeled with Cyanine-3 (Green) while spleen was labeled with Cyanine-5 (Red). cRNA was made by the single round amplification method. Keywords: repeat sample
2003-03-07 | GSE332 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE3972: Contribution of unique genes by individual cell lines to Universal Human Reference RNA GSE3973: Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls GSE3974: Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA Abstract: BACKGROUND: Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). Measuring signal at each spot as the ratio of experimental RNA to reference RNA targets, rather than relying on absolute signal intensity, decreases variability by normalizing signal output in any two-color hybridization experiment. RESULTS: Human, mouse and rat URR (UHRR, UMRR and URRR, respectively) were prepared from pools of RNA derived from individual cell lines representing different tissues. A variety of microarrays were used to determine percentage of spots hybridizing with URR and producing signal above a user defined threshold (microarray coverage). Microarray coverage was consistently greater than 80% for all arrays tested. We confirmed that individual cell lines contribute their own unique set of genes to URR, arguing for a pool of RNA from several cell lines as a better configuration for URR as opposed to a single cell line source for URR. Microarray coverage comparing two separately prepared batches each of UHRR, UMRR and URRR were highly correlated (Pearson's correlation coefficients of 0.97). CONCLUSION: Results of this study demonstrate that large quantities of pooled RNA from individual cell lines are reproducibly prepared and possess diverse gene representation. This type of reference provides a standard for reducing variation in microarray experiments and allows more reliable comparison of gene expression data within and between experiments and laboratories. Refer to individual Series
2006-03-07 | E-GEOD-4389 | biostudies-arrayexpress
Project description:Many library preparation methods are available for gene expression quantification. Here, we sequenced and analysed Universal Human Reference RNA (UHRR) prepared using Smart-Seq2, TruSeq (public data) and a protocol using unique molecular identifiers (UMIs) that all include the ERCC spike-in mRNAs to investigate the effects of amplification bias on expression quantification.
2016-05-13 | GSE75823 | GEO
Project description:Normal, premalignant and various histological subtypes of testicular germ cell tumor (TGCT) tissues were hybridized against Universal Human Reference RNA (Stratagene) onto Agilent 60mer oligo microarrays (GEO accession no GPL885). In vitro time series of two TGCT cell lines, NTERA2 and 2102Ep, treated with retinoic acid for 0, 3, and 7 days were also included. The data set (30 hybridizations) is particularly useful for comparisons between various histological subtypes of TGCT versus each other or versus normal testis. Keywords = 2102Ep Keywords = Agilent oligo microarrays Keywords = carcinoma in situ Keywords = choriocarcinoma Keywords = development Keywords = developmental biology Keywords = differenciation Keywords = embryogenesis Keywords = embryonal carcinoma Keywords = homo sapiens Keywords = human Keywords = human development Keywords = intratubular germ cell tumor Keywords = nonseminoma Keywords = NTera2 Keywords = pluripotency Keywords = pluripotent Keywords = retinoic acid Keywords = seminoma Keywords = teratocarcinoma Keywords = teratoma Keywords = testis Keywords = testicular germ cell tumor Keywords = testicular neoplasm Keywords = totipotency Keywords = totipotent Keywords = undifferentiated Keywords = universal human reference RNA (Stratagene) Keywords = yolk sac tumor Keywords: other
2005-07-01 | GSE1818 | GEO
Project description:3 fresh frozen Breast tumor from the University of North Carolina at Chapel Hill (UNC) were obtained from the UNC Tissue Procurement Facility under an IRB approved protocol. Each experimental sample was ssayed versus a common reference sample that was a modified version of the Stratagene Human Universal Reference (which was further augmented with a 1/10 amount of MCF7 mRNA and 1/10 amount of ME16C mRNA) Keywords = Agilent microarray Keywords = EGFR Keywords = keratin Keywords: parallel sample
2004-10-15 | GSE1319 | GEO