Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation

ABSTRACT: oligo-dT and random primed RNA-seq libraries were used to test an improved annotation of the zebrafish transcriptome

ORGANISM(S): Danio rerio

PROVIDER: GSE152759 | GEO | 2020/07/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation

Project description:Bulk RNA-seq data to assess an improved zebrafish transcriptome annotation

| PRJNA640350 | ENA

Drosophila melanogaster short read RNA

Project description:Drosophila melanogaster RNA sequencing with Illumina Genome Analyzer. High-throughput sequencing of Drosophila melanogaster RNAs. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 5 Samples: Single Stranded cDNA, Oligo-DT Primed, run using a 1, 2 and 4 p-mol concentration, no replicates. Double Stranded cDNA, Random Primed, run using a 2 p-mol concentration, 2 replicates.

2008-11-04 | E-GEOD-13441 | biostudies-arrayexpress

Serum Starvation/Refeeding RNA vs. RAP

Project description:Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics, signal-to-noise ratios, and interference between signals from mRNA isoforms. Individual sequences in LCRs are more highly represented than in the mRNA population from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo dT priming for target synthesis. An oligo dT-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo dT-primed target alone, as serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of spotted cDNA microarrays. Keywords: parallel sample

2005-05-17 | GSE2655 | GEO

Comparison of RNA-Seq libraries for degraded RNA between SMART-Seq, xGen and RamDA-Seq

Project description:Standard method of RNA-Seq captures mRNA by poly(A) capturing using Oligo dT beads, which is not suitable for degraded RNA. Here, we used three commercially available RNA-Seq library preparation kits (SMART-Seq, xGen Broad-range and RamDA-Seq) using random primer instead of Oligo dT beads. To evaluate the performance of these methods, we compared that the correla-tion, the number of detected expressing genes and the expression levels with Standard RNA-Seq method.SMART-Seq with rRNA depletion has relative advantages for RNA-Seq using low input and de-graded RNA.

2024-06-20 | GSE266382 | GEO

Serum Starvation/Refeeding RNA vs. RAP

2010-06-10 | E-GEOD-2655 | biostudies-arrayexpress

DEG9, a serine protease modulates cytokinins and light signaling by regulating the level of Arabidopsis Response Regulator 4

Project description:The Arabidopsis seedlings treated with 2M t-zeatin (CTK) for 30 minutes and then total RNA was extracted from Arabidopsis seedlings using TRIzol reagent (Invitrogen) and treated with RNase-free DNase I. The poly(A) mRNA was isolated using oligo (dT) beads. First-strand cDNA was subsequently generated using random hexamer-primed reverse transcription, followed by synthesis of the second-strand cDNA using RNaseH and DNA polymerase I. Then, single-end and paired-end RNA-seq libraries were prepared following Illumina's protocols and sequenced on the Illumina GA II platform.

2016-06-17 | E-MTAB-4603 | biostudies-arrayexpress

expression of SATs

Project description:Expression of the sense-antisense transcripts (SATs). Methods: The sequences of 60mer DNA specific to the sense and antisense genes were chosen by K.K. DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information. RNA was labeled and hybridized using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer's protocols. For labeling with random nanomers, we used the CyScribe First-Strand cDNA Labeling Kit (Amersham). The RNA samples used for microarray experiments were from mouse ES cells, SL10 cells (fibroblast cell line), brain, heart, and testis. The total RNA of brain, heart, and testis for array experiments was purchased from Ambion. The total RNA of ES and fibroblast cells was isolated using Trizol reagent (Invitrogen). The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized, and processed signals were obtained using Feature Extraction software (Agilent Technologies). Keywords: parallel sample

2005-03-31 | GSE2185 | GEO

Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

Project description:Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

| PRJNA613041 | ENA

tiling hen2 and mtr4-HEN2 is a cofactor of the nuclear exosome in Arabidopsis

Project description:til-ath-2011_3 - tiling hen2 and mtr4 - Identification and comparison of the RNA substrates that accumulate in hen2 and mtr4 mutants. Total RNA extracted from WT, hen2 and mtr4 mutants was used for oligo-dT primed cDNA preparation. Samples were hybridised to NimbleGen whole genome tiling arrays.

2013-06-30 | GSE48178 | GEO

Spatial total RNA sequencing of formalin-fixed paraffin embedded tissue by Spatial Random-seq

Project description:Current spatial transcriptomic methods have been widely used to resolve gene expression; however, these methods are limited to fresh or fresh-frozen samples due to unsuccess of oligo(dT) primers in degraded RNA samples. Here we develop a spatial random-sequencing (spRandom-seq) technology for Formalin-fixed paraffin-embedded (FFPE) tissues by capturing full-length total RNAs with random primers. This approach provides a powerful spatial platform for clinical FFPE specimens and promises enormous applications in biomedicine.

2023-12-31 | GSE247881 | 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