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Mus musculus

ABSTRACT: Chromatin position effects assayed by thousands of reporters integrated in parallel (RNA-Seq)

PROVIDER: PRJNA210802 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR927326.fastq.gz	Fastqsanger.gz
	SRR927327.fastq.gz	Fastqsanger.gz
	SRR927328.fastq.gz	Fastqsanger.gz
	SRR927329.fastq.gz	Fastqsanger.gz
	SRR927330.fastq.gz	Fastqsanger.gz

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Chromatin position effects assayed by thousands of reporters integrated in parallel (mPGK TRIP pools)

Project description:Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation. TRIP assay of mPGK promoter; 6 experiments, each with 2 technical replicates.

2013-08-16 | E-GEOD-48608 | biostudies-arrayexpress

Chromatin position effects assayed by thousands of reporters integrated in parallel (cell lines with mPGK IRs)

2013-08-16 | E-GEOD-49807 | biostudies-arrayexpress

Chromatin position effects assayed by thousands of reporters integrated in parallel (RNA-Seq)

Project description:Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation. mRNA profiles of 11 mouse embryonic cell lines each harboring multiple barcoded reporter constructs with mouse PGK promoter integrated at random positions in the genome, single replicate.

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Chromatin position effects assayed by thousands of reporters integrated in parallel (tet-Off TRIP pools)

Project description:Reporter genes integrated into the genome are a powerful tool to reveal effects of regulatory elements and local chromatin context on gene expression. However, so far such reporter assays have been of low throughput. Here we describe a multiplexing approach for the parallel monitoring of transcriptional activity of thousands of randomly integrated reporters. More than 27,000 distinct reporter integrations in mouse embryonic stem cells, obtained with two different promoters, show ~1,000-fold variation in expression levels. Data analysis indicates that lamina-associated domains act as attenuators of transcription, likely by reducing access of transcription factors to binding sites. Furthermore, chromatin compaction is predictive of reporter activity. We also found evidence for cross-talk between neighboring genes, and estimate that enhancers can influence gene expression on average over ~20 kb. The multiplexed reporter assay is highly flexible in design and can be modified to query a wide range of aspects of gene regulation. TRIP assay of tet-Off promotor; 4 experiments, each with 2 technical replicates. Each experiment was induced at 4 different concentrations of doxycycline.

2013-08-16 | E-GEOD-49806 | biostudies-arrayexpress

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