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TranscriptomicsAnnotating Low Abundance and Transient RNAs in Yeast using Ultra High-throughput Sequencing
Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing Reveals New Transcripts that are not Conserved Across Closely Related Yeast Species A complete description of the transcriptome of an organism is crucial for a comprehensive understand...
ORGANISM(S): Saccharomyces cerevisiae 
2008-12-18 | E-GEOD-11801 | biostudies-arrayexpress
GenomicsChip-Seq of human jurkat cell line to investigate genome-wide mapping of in vivo protein-DNA interactions
In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ...
ORGANISM(S): Homo sapiens 
2009-08-29 | E-GEOD-13047 | biostudies-arrayexpress
TranscriptomicsRNA-seq of rat dorsal root ganglia after ligation to investigate central nervous system transcriptomics in chronic pain using agnostic splice site discovery methods
The study pursued dual goals: To advance mRNA-seq bioinformatics towards unbiased transcriptome capture and to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We found that 12.4% of known genes were induced and 7% were sup...
ORGANISM(S): Rattus norvegicus 
2010-05-01 | E-GEOD-20895 | biostudies-arrayexpress
UnknownGiant tuning of ferroelectricity in single crystals by thickness engineering.
Not available
S-EPMC7556833 | biostudies-literature
TranscriptomicsFull-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
We assessed Smart-Seq, a new single-cell RNA-Seq library preparation method, on a variety of mouse and human RNA samples or cells. We generated RNA-Seq libraries for dilution series of MAQC reference RNA and mouse brain RNA to assess technical reproducibility, and for a variety of individual cells i...
ORGANISM(S): Homo sapiens 
2012-07-22 | E-GEOD-38495 | biostudies-arrayexpress
TranscriptomicsMultiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within com...
ORGANISM(S): Bacillus subtilis 
2011-08-26 | E-GEOD-31573 | biostudies-arrayexpress
TranscriptomicsAlternative Isoform Regulation in Human Tissue Transcriptomes
Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of...
ORGANISM(S): Homo sapiens 
2008-09-30 | E-GEOD-12946 | biostudies-arrayexpress
TranscriptomicsMutant analysis of C. elegans small RNAs, 5p-end-independent
These datasets profile the expression of small RNAs with 3p hydroxyls (including endo-siRNAs, miRNAs, and 21U-RNAs) in young adult worms from the wt and prg-1 mutant backgrounds. They were prepared using an approach that captures small RNAs independent of the covalent status of their 5p termini, as...
ORGANISM(S): Caenorhabditis elegans 
2008-06-15 | E-GEOD-11736 | biostudies-arrayexpress
TranscriptomicsHigh-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing
We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index...
ORGANISM(S): Danio rerio 
2010-09-30 | E-GEOD-20682 | biostudies-arrayexpress
TranscriptomicsMutant analysis of C. elegans small RNAs with 5p monophosphates
These datasets profile the expression of small RNAs with 5p monophosphates and 3p hydroxyls (including miRNAs, 21U-RNAs) in young adult worms from the wt, prg-1 mutant, and fog-2 mutant backgrounds. These datasets were prepared in the Craig C. Mello laboratory using T4 RNA ligase 1. Keywords: miRNA...
ORGANISM(S): Caenorhabditis elegans 
2008-06-15 | E-GEOD-11735 | biostudies-arrayexpress
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