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Series GSE48608 Query DataSets for GSE48608
Status Public on Aug 16, 2013
Title Chromatin position effects assayed by thousands of reporters integrated in parallel (mPGK TRIP pools)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary 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.
 
Overall design TRIP assay of mPGK promoter; 6 experiments, each with 2 technical replicates.
 
Contributor(s) Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W, Filion GJ, de Ridder J, Berns A, Wessels LF, van Lohuizen M, van Steensel B
Citation(s) 23953119
Submission date Jul 08, 2013
Last update date May 15, 2019
Contact name Bas van Steensel
E-mail(s) b.v.steensel@nki.nl
Phone + 31 20 512 2040
Fax +31 20 669 1383
URL http://www.nki.nl/nkidep/vansteensel
Organization name Netherlands Cancer Institute
Department division of Molecular Biology
Lab van Steensel group
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066 CX
Country Netherlands
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (72)
GSM1207287 mPGK-A expression_counts, repl_1, PCR 1
GSM1207288 mPGK-A expression_counts, repl_1, PCR 2
GSM1207289 mPGK-A expression_counts, repl 2, PCR 1
This SubSeries is part of SuperSeries:
GSE48606 Chromatin position effects assayed by thousands of reporters integrated in parallel
Relations
BioProject PRJNA214967
SRA SRP028732

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Supplementary file Size Download File type/resource
GSE48608_Data_File_S1.txt.gz 381.4 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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