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GEO help: Mouse over screen elements for information. |
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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
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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.
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Overall design |
TRIP assay of mPGK promoter; 6 experiments, each with 2 technical replicates.
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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 |
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Submission date |
Jul 08, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Bas van Steensel |
E-mail(s) |
b.v.steensel@nki.nl
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Phone |
+ 31 20 512 2040
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Fax |
+31 20 669 1383
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URL |
http://www.nki.nl/nkidep/vansteensel
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Organization name |
Netherlands Cancer Institute
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Department |
division of Molecular Biology
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Lab |
van Steensel group
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Street address |
Plesmanlaan 121
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City |
Amsterdam |
ZIP/Postal code |
1066 CX |
Country |
Netherlands |
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Platforms (1) |
GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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Samples (72)
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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 |
GSM1207290 |
mPGK-A expression_counts, repl 2, PCR 2 |
GSM1207291 |
mPGK-A normalization_counts, repl 1, PCR 1 |
GSM1207292 |
mPGK-A normalization_counts, repl 1, PCR 2 |
GSM1207293 |
mPGK-A normalization_counts, repl 2, PCR 1 |
GSM1207294 |
mPGK-A normalization_counts, repl 2, PCR 2 |
GSM1207295 |
mPGK-A mapping, repl 1, PCR 1 |
GSM1207296 |
mPGK-A mapping, repl 1, PCR2 |
GSM1207297 |
mPGK-A mapping, repl 2, PCR1 |
GSM1207298 |
mPGK-A mapping, repl 2, PCR 2 |
GSM1207299 |
mPGK-B expression_counts, repl_1, PCR 1 |
GSM1207300 |
mPGK-B expression_counts, repl_1, PCR 2 |
GSM1207301 |
mPGK-B expression_counts, repl 2, PCR 1 |
GSM1207302 |
mPGK-B expression_counts, repl 2, PCR 2 |
GSM1207303 |
mPGK-B normalization_counts, repl 1, PCR 1 |
GSM1207304 |
mPGK-B normalization_counts, repl 1, PCR 2 |
GSM1207305 |
mPGK-B normalization_counts, repl 2, PCR 1 |
GSM1207306 |
mPGK-B normalization_counts, repl 2, PCR 2 |
GSM1207307 |
mPGK-B mapping, repl 1, PCR 1 |
GSM1207308 |
mPGK-B mapping, repl 1, PCR2 |
GSM1207309 |
mPGK-B mapping, repl 2, PCR1 |
GSM1207310 |
mPGK-B mapping, repl 2, PCR 2 |
GSM1207311 |
mPGK-C expression_counts, repl_1, PCR 1 |
GSM1207312 |
mPGK-C expression_counts, repl_1, PCR 2 |
GSM1207313 |
mPGK-C expression_counts, repl 2, PCR 1 |
GSM1207314 |
mPGK-C expression_counts, repl 2, PCR 2 |
GSM1207315 |
mPGK-C normalization_counts, repl 1, PCR 1 |
GSM1207316 |
mPGK-C normalization_counts, repl 1, PCR 2 |
GSM1207317 |
mPGK-C normalization_counts, repl 2, PCR 1 |
GSM1207318 |
mPGK-C normalization_counts, repl 2, PCR 2 |
GSM1207319 |
mPGK-C mapping, repl 1, PCR 1 |
GSM1207320 |
mPGK-C mapping, repl 1, PCR2 |
GSM1207321 |
mPGK-C mapping, repl 2, PCR1 |
GSM1207322 |
mPGK-C mapping, repl 2, PCR 2 |
GSM1207323 |
mPGK-D expression_counts, repl_1, PCR 1 |
GSM1207324 |
mPGK-D expression_counts, repl_1, PCR 2 |
GSM1207325 |
mPGK-D expression_counts, repl 2, PCR 1 |
GSM1207326 |
mPGK-D expression_counts, repl 2, PCR 2 |
GSM1207327 |
mPGK-D normalization_counts, repl 1, PCR 1 |
GSM1207328 |
mPGK-D normalization_counts, repl 1, PCR 2 |
GSM1207329 |
mPGK-D normalization_counts, repl 2, PCR 1 |
GSM1207330 |
mPGK-D normalization_counts, repl 2, PCR 2 |
GSM1207331 |
mPGK-D mapping, repl 1, PCR 1 |
GSM1207332 |
mPGK-D mapping, repl 1, PCR2 |
GSM1207333 |
mPGK-D mapping, repl 2, PCR1 |
GSM1207334 |
mPGK-D mapping, repl 2, PCR 2 |
GSM1207335 |
mPGK-E expression_counts, repl_1, PCR 1 |
GSM1207336 |
mPGK-E expression_counts, repl_1, PCR 2 |
GSM1207337 |
mPGK-E expression_counts, repl 2, PCR 1 |
GSM1207338 |
mPGK-E expression_counts, repl 2, PCR 2 |
GSM1207339 |
mPGK-E normalization_counts, repl 1, PCR 1 |
GSM1207340 |
mPGK-E normalization_counts, repl 1, PCR 2 |
GSM1207341 |
mPGK-E normalization_counts, repl 2, PCR 1 |
GSM1207342 |
mPGK-E normalization_counts, repl 2, PCR 2 |
GSM1207343 |
mPGK-E mapping, repl 1, PCR 1 |
GSM1207344 |
mPGK-E mapping, repl 1, PCR2 |
GSM1207345 |
mPGK-E mapping, repl 2, PCR1 |
GSM1207346 |
mPGK-E mapping, repl 2, PCR 2 |
GSM1207347 |
mPGK-F expression_counts, repl_1, PCR 1 |
GSM1207348 |
mPGK-F expression_counts, repl_1, PCR 2 |
GSM1207349 |
mPGK-F expression_counts, repl 2, PCR 1 |
GSM1207350 |
mPGK-F expression_counts, repl 2, PCR 2 |
GSM1207351 |
mPGK-F normalization_counts, repl 1, PCR 1 |
GSM1207352 |
mPGK-F normalization_counts, repl 1, PCR 2 |
GSM1207353 |
mPGK-F normalization_counts, repl 2, PCR 1 |
GSM1207354 |
mPGK-F normalization_counts, repl 2, PCR 2 |
GSM1207355 |
mPGK-F mapping, repl 1, PCR 1 |
GSM1207356 |
mPGK-F mapping, repl 1, PCR2 |
GSM1207357 |
mPGK-F mapping, repl 2, PCR1 |
GSM1207358 |
mPGK-F mapping, repl 2, PCR 2 |
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This SubSeries is part of SuperSeries: |
GSE48606 |
Chromatin position effects assayed by thousands of reporters integrated in parallel |
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Relations |
BioProject |
PRJNA214967 |
SRA |
SRP028732 |
Supplementary file |
Size |
Download |
File type/resource |
GSE48608_Data_File_S1.txt.gz |
381.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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