Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Optimised linear amplification method for whole transcriptome analysis from low quantity RNA isolated from archival FFPE tissue

ABSTRACT: Optimised linear amplification method for whole transcriptome analysis from low quantity RNA isolated from archival FFPE tissue

PROVIDER: PRJNA948833 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23972400.fastq.gz	Fastqsanger.gz
	SRR23972401.fastq.gz	Fastqsanger.gz
	SRR23972402.fastq.gz	Fastqsanger.gz
	SRR23972403.fastq.gz	Fastqsanger.gz
	SRR23972404.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 21

Similar Datasets

Optimised linear amplification method for whole transcriptome analysis from low quantity RNA isolated from archival FFPE tissue

Project description:The study described a comprehensive high-fidelity method to successfully amplify low starting amounts of RNA extracted from FFPE tissue obtained from bronchial biopsies. Both amplified and unamplified RNA resulted in comparable gene expression for lung cancer and asthma samples.

2023-03-30 | GSE228217 | GEO

Archival chromatin sequencing in eastern water dragon museum specimens

Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.

2024-03-01 | GSE256157 | GEO

Transcription profiling to analyse the effect of the amount of human input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification

Project description:This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations.

2005-09-30 | E-SMDB-1609 | biostudies-arrayexpress

RNA-seq from archival FFPE Breast Cancer samples: Molecular Pathway Fidelity and Novel Discovery

Project description:Archival Formalin-Fixed Paraffin Embedded (FFPE) tissue represents an abundant and more easily transferable source of patient tissue than live specimens. Furthermore cancer FFPE tissue deposited at major cancer research institutes is often paired with survival data increasing the value of biomarker and prediction based research from these samples. However the known fragility of RNA and artifacts introduced through the processes of tissue preservation and storage introduce the possibility of unfaithful RNA expression signatures from these sources. To evaluate this we established an RNA isolation, library prepration and data analysis pipeline at Oregon Health and Science University to evaluate the fidelity of RNA expression profiles from FFPE tissues utilizing gene and pathway expression comparisons between ER positive and ER negative samples in archival FFPE specimens compared to those obtained from public available data sets of fresh specimens.

2019-11-26 | GSE130397 | GEO

Validation of the linear amplification of single bovine embryos

Project description:To generate expression profiles from single embryos, a protocol for linear amplification of RNA was developed on the basis of Baugh et al. (15). Linear amplification enabled production of sufficient amounts of aRNA for the microarray experiments and has been shown to reliably amplify the initial mRNA population (15, 18-20). Approximately 5 ng of total RNA can be isolated from a blastocyst-stage embryo (21); therefore, it was necessary to carry out multiple rounds of amplification. To test the reproducibility and fidelity of the amplification procedure, a validation experiment was conducted using RNA from the kidney tissue of a newborn calf. Two replicates of the bovine kidney RNA were amplified and hybridized to the microarray. Comparisons were made between aRNA (rounds 1, 2, and 3) and unamplified RNA. Keywords: cDNA microarray

2005-11-30 | GSE3569 | GEO

Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded (FFPE) Samples

Project description:Use of archival resources has been limited to date by inconsistent methods for genomic profiling of degraded RNA from formalin-fixed paraffin-embedded (FFPE) samples. RNA-seq offers a novel way to address this problem. In this study we evaluated transcriptomic dose responses using RNA-seq in paired FFPE and frozen (FROZ) samples from two archival studies in mice, one recent (<2 years old) and the other older (>20 years old). Experimental treatments included di(2-ethylhexyl)phthalate (DEHP) and dichloroacetic acid (DCA) for the <2 and >20 year-old studies, respectively. Total RNA was ribodepleted and sequenced using the Illumina HiSeq platform. In the recent study, FFPE samples showed high concordance in total reads (98% vs FROZ), fold-change values of differentially expressed genes (DEGs) (R2 = 0.99), highly enriched target pathways (90% overlap with FROZ), and benchmark dose estimates for preselected target genes (-2% overall vs FROZ). In contrast, RNA-seq data from older FFPE samples had lower total reads (70% vs FROZ) and poor concordance in global DEGs and pathways. Despite a 99% loss of counts, dose responses were still evident for target genes in FFPE samples and positively correlated with paired FROZ samples. These findings highlight potential variability in the quality of RNA-seq data from FFPE samples. More recent FFPE samples were highly similar to FROZ samples in sequencing quality metrics, DEG profiles, and dose-response parameters, while further methods development is needed for older or lower-quality FFPE samples. This work should help broaden the use of archival resources in both chemical safety and translational science.

2016-08-30 | GSE78962 | GEO

Effect of ligase on T7 based RNA linear amplification

Project description:Zhao et al. Amplification Table 3 This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3561 | GEO

Effect of column cleanup on T7 based RNA linear amplification

Project description:Zhao et al. Amplification Table 4 This experiment was designed to evaluate the effect of column cleanup on the fidelity and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with or without G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3562 | GEO

Single-tube Linear DNA amplification (LinDA) for robust ChIP-seq

Project description:Genome-wide profiling of transcription factors based on massive parallel sequencing of immunoprecipitated chromatin (ChIP-seq) requires nanogram amounts of DNA. Here we describe a high-fidelity, single-tube linear DNA amplification method (LinDA) for ChIP-seq and reChIP-seq with picogram DNA amounts obtained from a few thousand cells. This amplification technology will facilitate global analyses of transcription-factor binding and chromatin with very small cell populations, such as stem or cancer-initiating cells.

2011-10-11 | GSE32332 | GEO

Effect of the amount of input total RNA on T7 amplification

Project description:Zhao et al. Amplification Table 9 This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3557 | 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