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TranscriptomicsTranscript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms
We introduce an approach to transcript discovery coupled with a statistical model for RNA-Seq experiments that produces estimates of transcript abundances. Our algorithms are implemented in an open source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed more than 430 m...
ORGANISM(S): Mus musculus 
2010-04-14 | E-GEOD-20846 | biostudies-arrayexpress
GenomicsDynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity [ChIP-Seq]
T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using deep sequencing RNA-seq and ChIP-seq methods to track genome-wide shifts in transcripti...
ORGANISM(S): Mus musculus 
2012-04-13 | E-GEOD-31233 | biostudies-arrayexpress
TranscriptomicsDynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity [RNA-Seq]
T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using deep sequencing RNA-seq and ChIP-seq methods to track genome-wide shifts in transcripti...
ORGANISM(S): Mus musculus 
2012-04-13 | E-GEOD-31234 | biostudies-arrayexpress
UnknownOral Immunotherapy Using Probiotic Ice Cream Containing Recombinant Food-Grade Lactococcus lactis Which Inhibited Allergic Responses in a BALB/c Mouse Model.
Not available
S-EPMC7532367 | biostudies-literature
TranscriptomicsRNA-seq from ENCODE/Caltech (Mouse)
RNA-seq is a method for mapping and quantifying the transcriptome of any organism that has a genomic DNA sequence assembly (Mortazavi et al., 2008). RNA-seq is performed by reverse-transcribing an RNA sample into cDNA, followed by high-throughput DNA sequencing, which was done here on the Illumina H...
ORGANISM(S): Mus musculus 
2012-05-09 | E-GEOD-37909 | biostudies-arrayexpress
UnknownWhat is the best cutoff point of leukocyte esterase for diagnosis of periprosthetic joint infections? a systematic review and meta-analysis.
Not available
S-EPMC12323279 | biostudies-literature
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
UnknownDynamic Gene Regulatory Networks of Human Myeloid Differentiation.
Not available
S-EPMC5490374 | biostudies-literature
TranscriptomicsRNA-seq from ENCODE/Caltech
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (mailto:georgi@caltech.edu for data coordination/informatics/experimental questions, mailto:diane@caltech.edu for informatics questions, mailto:bawilli_91125@yahoo.com for experimental...
ORGANISM(S): Homo sapiens 
2012-07-12 | E-GEOD-33480 | biostudies-arrayexpress
TranscriptomicsDe novo transcriptome analysis profiles gene expression underlying seasonal polyphenism in butterfly wing patterns
In the eastern United States the buckeye butterfly, Junonia coenia, shows a seasonal wing color polyphenism where adults emerging in the spring are pale brown, while those emerging in the autumn are dark red. This variation can be artificially induced in laboratory colonies, thus making J. coenia a ...
ORGANISM(S): Junonia coenia 
2014-02-15 | E-GEOD-54819 | biostudies-arrayexpress
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