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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling to analyse the effect of the date of preparation of human polyA RNA

ABSTRACT: This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-1613 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis.

Zhao Hongjuan H Hastie Trevor T Whitfield Michael L ML Børresen-Dale Anne-Lise AL Jeffrey Stefanie S SS

BMC genomics 20021030 1

<h4>Background</h4>T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays.<h4>Results</h4>Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified ...[more]

PMID: 12445333

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Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA

Project description:Zhao et al. Amplification BC2 uM This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. Keywords: replicate_design

2005-11-04 | GSE3559 | GEO

Variation in cDNA microarray analysis of gene expression using unamplified poly(A)+ RNA

2005-11-03 | E-GEOD-3559 | biostudies-arrayexpress

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

Mass spectrometry approach to identify mitochondrial poly(A) RNA interacting proteins

Project description:To identify mitochondrial RNA-interacting proteins, we developed three related mass spectrometry based methods. In the first method, called mitochondrial crosslinking (MXL), mitochondria of 4-thiouridine labelled cells were isolated, exposed to UV-light and poly(A) RNA was isolated. In the second method, called whole cell crosslinking (WCXL), 4-thiouridine labelled cells were first exposed to UV-light, subsequently mitochondria were isolated followed by a poly(A) RNA extraction. The third method, called ethidium bromide whole cell crosslinking (WCXL_EtBr), is exactly the same as the WCXL method, but the cells are cultured with ethidium bromide to reduce the amount of mitochondrial RNA. In all methods poly(A) RNA was degraded and proteins in the sample were digested and identified using mass spectrometry.

2019-10-15 | PXD014957 | Pride

Identification of polyA sites in Drosophila melanogaster

2011-11-23 | GSE33905 | GEO

Transcription profiling of different tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor

Project description:This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup.

2006-06-06 | E-SMDB-1764 | biostudies-arrayexpress

Correlation between expression levels of different tumors measured by poly(A)+RNA and aRNA

Project description:Zhao et al. Amplification Table 7 This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

2005-11-04 | GSE3563 | 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

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Identification of polyA sites in Drosophila melanogaster

Project description:The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf RNA from 29 dissected Drosophila melanogaster tissues (in duplicate) were used to prepare polyA enriched RNA-Seq libraries. Briefly, total RNA was poly(A) selected, fragmented, and ligated to 5' and 3' RNA linkers. These libraries were amplified using Illumina paired-end primers, and subsequently reamplified using a 3' primer complementary to the 3' adapter but containing 6 Ts at the 3' end. The libraries were also multiplexed and up to 12 samples mixed per lane and sequenced on an Illumina GAIIx using paired-end 76 bp reads, or an illumina HiSeq 2000 using paired-end 100 bp reads. All reads were mapped to the Drosophila melanogaster genome to identify unmapped reads. Unmapped reads containing at least 10 A residues at the 3' end were identified, the terminal A residues trimmed, realigned to the genome to identify uniquely mapped reads. Such reads were identified as polyA spanning reads

2011-11-23 | E-GEOD-33905 | biostudies-arrayexpress

polyA mRNA RNA-seq from fibroblast of lung (ENCSR000CPM)

Project description:The libraries contained in this experiment come from lung fibroblast primary whole cells, NHLF isolated from independent donors. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted Poly-A+ RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-03-18 | GSE78595 | GEO

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