Browse
Submit Data
Databases
API
Help

Dataset Information

10 Views

6 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 1003

MDACC-Yale

ABSTRACT: Organisation EGAO00000000270

PROVIDER: EGAO00000000270 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments.

Qi Yuan Y Liu Xiuping X Liu Chang-Gong CG Wang Bailing B Hess Kenneth R KR Symmans W Fraser WF Shi Weiwei W Pusztai Lajos L

PloS one 20150702 7

Nucleotide alterations detected by next generation sequencing are not always true biological changes but could represent sequencing errors. Even highly accurate methods can yield substantial error rates when applied to millions of nucleotides. In this study, we examined the reproducibility of nucleotide variant calls in replicate sequencing experiments of the same genomic DNA. We performed targeted sequencing of all known human protein kinase genes (kinome) (~3.2 Mb) using the SOLiD v4 platform. ...[more]

PMID: 26136146

Similar Datasets

Yale

Project description:Organisation EGAO00000000643

| EGAO00000000643 | EGA

Yale Cancer Center, Yale School of Medicine, Yale University

Project description:Organisation EGAO00000000395

| EGAO00000000395 | EGA

Yale University

Project description:Organisation EGAO00000000644

| EGAO00000000644 | EGA

MDACC

Project description:Organisation EGAO00000000085

| EGAO00000000085 | EGA

Yale University School of Medicine

Project description:Organisation EGAO00000000959

| EGAO00000000959 | EGA

MDACC-Yale-breast-cancer

Project description:Data Access Committee EGAC00001000298

| EGAC00001000298 | EGA

MDACC Ovarian Cancer Moonshot

Project description:Molecular analysis of clinically defined subsets of high grade serous ovarian caner

| PRJEB32565 | ENA

Yale Triple Negative Breast Cancer Cohort

Project description:Triple negative breast cancer (TNBC) is characterized by high proliferation, poor differentiation and a poor prognosis due to high rates of recurrence. Despite lower overall incidence African American (AA) patients suffer from higher breast cancer mortality in part due to the higher proportion of TNBC cases among AA patients compared to European Americans (EA). It was recently shown that the clinical heterogeneity of TNBC is reflected by distinct transcriptional programs with distinct drug response profiles in preclinical models. In this study, we used gene expression profiling and immunohistochemistry to eluicidate potential differences between TNBC tumors of EA and AA patients on a molecular level. WG-DASL experiment of 90 FFPE samples of ER, PR and HER2 (triple) negative breast cancer samples diagnosed between 1987 and 2007. Invasive disease was identified on H&E sections by the study pathologist and one to three 1.5 mm cores were punched from the top down in the designated tumor areas of each FFPE block. The cores were deparaffinized with xylene at 50°C for 3 minutes. RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Applied Biosystems) following the manufacturer's protocol. The isolated RNA was hybridized to Whole-Genome DASL (HumanRef8 V 3.0, Illumina) at the Yale Center for Genome Analysis. 90 primary tumor RNA samples from 90 patients were adequate for analysis and passed Quality control.

| S-ECPF-GEOD-46581 | biostudies-other

The Yale Craving Scale: Development and psychometric properties.

Project description:The current study presents a psychometric evaluation of the Yale Craving Scale (YCS), a novel measure of craving for cigarettes and alcohol, respectively. The YCS is the first craving measure to use a generalized Labeled Magnitude Scale (gLMS) as the scoring format, which facilitates between-group comparisons of subjective craving and eliminates ceiling effects by assessing the full range of imaginable sensation intensities.Psychometric evaluations of the YCS for use with cigarettes (YCS Smoking) and alcohol (YCS Drinking) included assessments of latent factor structure, internal consistency, ceiling effects, and test-criterion relationships. Study samples included 493 treatment-seeking smokers and 213 heavy drinkers.Factor analyses of the 5-item YCS Smoking and Drinking scores confirmed a 1-factor scale. The YCS Smoking and Drinking scores evidenced: (1) good internal consistency, (2) scalar measurement invariance within several subgroups (e.g., smoking/drinking status; nicotine/alcohol dependence), (3) convergent relationships with extant craving measures, and (4) concurrent relationships with smoking/drinking outcomes.These results suggest that the YCS represents a psychometrically sound scale for assessing smoking and drinking urges in dependent populations.

| S-EPMC4834029 | biostudies-literature

ENCODE Spike-In, Yale Group

Project description:Simulated ChIP DNA labeled by random priming with Klenow; Samples were "Undiluted" and not amplified prior to labeling. Keywords: other For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

2007-12-28 | GSE10004 | GEO

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