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GenomicsGenome-wide maps of HLH-1 binding in muscle-enriched embryos.
To investigate the structure of the bodywall muscle differentiation network, we sought to both identify what role HLH-1 binding has in this regulation. We mapped the relationship between the regulatory targets and HLH-1 binding, as measured by ChIP-seq in animals enriched for bodywall muscle tissue ...
ORGANISM(S): Caenorhabditis elegans 
2012-06-21 | E-GEOD-28561 | 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
GenomicsTranscription Factor Binding Sites by ChIP-seq from ENCODE/Caltech
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Barbara Wold mailto:woldb@caltech.edu, Georgi K. Marinov mailto:georgi@caltech.edu, Diane Trout mailto:diane@caltech.edu). If you have questions about the Genome Browser track associa...
ORGANISM(S): Mus musculus 
2012-04-13 | E-GEOD-36024 | 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
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
TranscriptomicsSingle Cell RNA-Seq
RNA-seq transcriptome measurements are typically performed by isolating RNA from large numbers of cells in culture or tissues. While highly informative, such experiments mask the variability in gene expression patterns that exists between individual cells. To gain insight into the dynamics of gene e...
ORGANISM(S): Homo sapiens 
2013-11-21 | E-GEOD-44618 | biostudies-arrayexpress
TranscriptomicsChIP-chip mapping of twist, dorsal, snail, weckle in Drosophila embryos
We performed ChIP-chip analysis using sheared chromatin isolated from Drosophila embryos of 1-3 hours in age. Keywords: high-resolution tiling array, drosophila, twist, dorsal, snail, weckle ChIP-chip of twist, dorsal, snail, and weckle
ORGANISM(S): Drosophila melanogaster 
2011-02-28 | E-GEOD-26285 | biostudies-arrayexpress
GenomicsHistone Modifications by ChIP-seq from ENCODE/Caltech
This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Barbara Wold mailto:woldb@caltech.edu, Georgi K. Marinov mailto:georgi@caltech.edu, Diane Trout mailto:diane@caltech.edu). If you have questions about the Genome Browser track associa...
ORGANISM(S): Mus musculus 
2012-04-19 | E-GEOD-36023 | biostudies-arrayexpress
TranscriptomicsSingle-cell transcriptional landscape of human embryonic limb development
Human limbs emerge during the fourth post-conception week as mesenchymal buds, which develop into fully formed limbs over the subsequent months. This process is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common....
ORGANISM(S): Homo sapiens 
2022-04-15 | E-MTAB-8813 | biostudies-arrayexpress
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