Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

ABSTRACT: Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue.

ORGANISM(S): Homo sapiens

PROVIDER: GSE28475 | GEO | 2012/04/03

SECONDARY ACCESSION(S): PRJNA139321

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples

Project description:Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue. IVT- and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates. A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor. The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).

2012-04-02 | E-GEOD-28475 | biostudies-arrayexpress

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Assessment of cross-platform concordance.

Project description:We examine the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays.

2013-05-01 | GSE36147 | GEO

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: Assessment of cross-platform concordance.

Project description:We examine the concordance between miRNA-seq and cDNA-mediated annealing, selection, extension, and ligation (DASL) miRNA assays. We profiled two technically replicated FFPE specimens on both DASL and RNA-seq. This submission represents the RNA-seq component of study. The DASL samples used in the study are GSM876557, GSM876558, GSM876564, and GSM876565.

2013-05-01 | E-GEOD-36147 | biostudies-arrayexpress

Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded (FFPE)and Fresh Frozen (FF) Breast Cancer samples

Project description:Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order to do that, we analyzed 20 FFPE breast cancer samples and 20 FF (Fresh Frozen) matched samples with the Illumina Whole Genome DASL platform for a genome-wide expression profiling.

2011-09-05 | E-TABM-1081 | biostudies-arrayexpress

Genome-wide expression assay comparison across frozen and fixed postmortem brain tissue samples.

Project description:Gene expression assays have been shown to yield high quality genome-wide data from partially degraded RNA samples. However, these methods have not yet been applied to postmortem human brain tissue, despite their potential to overcome poor RNA quality and other technical limitations inherent in many assays. We compared cDNA-mediated annealing, selection, and ligation (DASL)- and in vitro transcription (IVT)-based genome-wide expression profiling assays on RNA samples from artificially degraded reference pools, frozen brain tissue, and formalin-fixed brain tissue.The DASL-based platform produced expression results of greater reliability than the IVT-based platform in artificially degraded reference brain RNA and RNA from frozen tissue-based samples. Although data associated with a small sample of formalin-fixed RNA samples were poor when obtained from both assays, the DASL-based platform exhibited greater reliability in a subset of probes and samples.Our results suggest that the DASL-based gene expression-profiling platform may confer some advantages on mRNA assays of the brain over traditional IVT-based methods. We ultimately consider the implications of these results on investigations of neuropsychiatric disorders.

| S-EPMC3179967 | biostudies-literature

Gene Expression Profiling of Fixed Tissues of Lymph Node Metastasis in Hepatocellular Carcinoma

Project description:RNA was extracted from formalin-fixed specimens of paired intratumoral and peritumoral tissues of patients with lymph node-positive (n=20) or negative (n=20) HCC. A cDNA-mediated annealing, selection, extension, and ligation assay was performed with an array of 502 known cancer-related genes to identify differentially expressed genes in 80 RNA samples. Total RNA was purified from the tissue specimens using the High Pure RNA Paraffin Kit according to the manufacturer’s protocol. DASL experiments were performed to identify genes that were differentially expressed between the lymph node metastasis (LNM) and non-lymph node metastasis (NLNM) groups of matched intratumoral and peritumoral tissues by using A cDNA-mediated annealing, selection, extension, and ligation assay.

2011-08-03 | E-GEOD-28248 | biostudies-arrayexpress

Alzheimer's disease postmortem brain

Project description:LC-MS/MS data for 96 postmortem prefrontal brain samples obtained from BDR cohort

2024-06-30 | MSV000095192 | MassIVE

Gene expression data from malignant gliomas

Project description:Formalin-fixed, paraffin-embedded (FFPE) samples of varying grade (II-IV) malignant gliomas were measured by Illumina cDNA-mediated Annealing, Selection, extension and ligration (DASL) platform. DASL platform was selected for its specialized design for partially degraded RNA.

2014-02-13 | GSE54004 | GEO

Bulk RNA-seq of postmortem human prefrontal cortex and cerebellum brain tissues

Project description:Analyzing brain region differences for postmortem Alzheimer's disease tissues.

2024-06-30 | E-MTAB-14167 | biostudies-arrayexpress

Single-nucleus transcriptomic analysis in the prefrontal cortex of postmortem human brain

Project description:These data describe single-nucleus RNA sequencing in postmortem human brain.

2022-06-17 | GSE205642 | GEO