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GenomicsPol II (Rpb3) ChIP-seq in Drosophila melanogaster S2 cells
Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoter...
ORGANISM(S): Drosophila melanogaster 
2012-10-25 | E-GEOD-23542 | biostudies-arrayexpress
TranscriptomicsGRO-seq of Drosophila embryos at 2-2.5 hours and 3-3.5 hours after egg laying (AEL)
The transition in developmental control from maternal to zygotic gene products marks a critical step in early embryogenesis. Here, we use GRO-seq analysis to map the genome-wide RNA polymerase distribution during the Drosophila maternal to zygotic transition. This analysis unambiguously identifies t...
ORGANISM(S): Drosophila melanogaster 
2013-05-28 | E-GEOD-41611 | biostudies-arrayexpress
TranscriptomicsNascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
RNA polymerases are highly regulated molecular machines. We present a method (GRO-seq) that maps the position, amount, and orientation of transcriptionally-engaged RNA polymerases genome-wide. In this method, nuclear run-on RNAs are subjected to large-scale parallel sequencing and mapped to the gen...
ORGANISM(S): Homo sapiens 
2008-12-04 | E-GEOD-13518 | biostudies-arrayexpress
TranscriptomicsDevelopment of GRO-cap (GRO-seq followed by 5'-cap enrichment) to map transcription start sites in C. elegans
Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends...
ORGANISM(S): Caenorhabditis elegans 
2013-06-18 | E-GEOD-43085 | biostudies-arrayexpress
TranscriptomicsSignaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: Estrogen dependent signaling in MCF-7 cells
We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pa...
ORGANISM(S): Homo sapiens 
2013-04-10 | E-GEOD-41324 | biostudies-arrayexpress
TranscriptomicsUsing GRO-seq experiments to determine the mechanism of C. elegans dosage compensation's control of transcription
Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends...
ORGANISM(S): Caenorhabditis elegans 
2013-06-18 | E-GEOD-43084 | biostudies-arrayexpress
TranscriptomicsGlobal Analysis of the Immediate Transcriptional Effects of Estrogen Signaling Reveals a Rapid, Extensive, and Transient Response
We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using Global Run-On and sequencing (GRO-seq). We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. ...
ORGANISM(S): Homo sapiens 
2011-05-05 | E-GEOD-27463 | biostudies-arrayexpress
GenomicsBinding of the C. elegans dosage compensation complex protein DPY-27
Dosage Compensation is required to correct for uneven gene dose between the sexes. We utilized global run-on sequencing (GRO-seq) to examine how Caenorhabditis elegans dosage compensation reduces transcription of X-linked genes. To facilitate these experiments, we required accurate 5M-bM-^@M-^Y-ends...
ORGANISM(S): Caenorhabditis elegans 
2013-06-18 | E-GEOD-43086 | biostudies-arrayexpress
TranscriptomicsSignaling Pathways Deferentially Affect RNA Polymerase II Initiation, Pausing, and Elongation in Human Cells: TNF-alpha dependent signaling in AC16 cells
We used Global Run-on and Sequencing (GRO-seq) to measure the rate of transcription elongation by RNA polymerase II (Pol II) following gene activation. We observed that Pol II elongation rates can vary as much as 4-fold at different genomic loci and in response to two distinct cellular signaling pa...
ORGANISM(S): Homo sapiens 
2013-04-10 | E-GEOD-41323 | biostudies-arrayexpress
TranscriptomicsGRO-seq in HeLa cells
Mapping the nascent RNA transcriptome of HeLa cells with GRO-seq Standard GRO-seq assay from two replicates in HeLa cells
ORGANISM(S): Homo sapiens 
2014-10-04 | E-GEOD-62046 | biostudies-arrayexpress
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