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| Status |
Public on Jan 12, 2015 |
| Title |
Transcriptome reorganization of gene-rewired Escherichia coli cells in response to histidine depletion |
| Organism |
Escherichia coli |
| Experiment type |
Expression profiling by genome tiling array
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| Summary |
An assortment of genetically engineered Escherichia coli strains of the rewired gene regulation were used to study whether the cells could adapt to the environmental changes without the evolved gene regulatory machinaries. These E. coli strains had a synthetic gene circuit comprising a rewried gene that natively located within the His opeon. The cells growing under histidine supplied or depleted conditions were subjected to the macrioarray analysis. Multilevel analyses were performed to evaluate the global reorganization of gene expression in response to histidine depletion. A common pattern in transcriptome was observed in the adpative cells, indicating a survival strategy of "stochastic adaptation with regular transcriptome reorganization".
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| Overall design |
The genetically engineered strains of rewired genes and the control strain of the native gene regulation were grown in the presence and absence of histidine, and the cells within the exponetially growing phase were collected for the microarray analysis. Temproal changes in response to histidine depletion were also investigated. Every 3 biological replications for each condition were performed. Total 90 array assays were reported here.
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| Contributor(s) |
Murakami Y, Ying B, Yomo T |
| Citation(s) |
25564530 |
| Submission date |
Mar 10, 2014 |
| Last update date |
Mar 18, 2015 |
| Contact name |
Bei-Wen Ying |
| E-mail(s) |
ying.beiwen.gf@u.tsukuba.ac.jp
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| Phone |
81 29 853 6633
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| Organization name |
University of Tsukuba
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| Street address |
1-1-1 Tennoudai
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8572 |
| Country |
Japan |
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| Platforms (1) |
| GPL13336 |
Affymetrix Escherichia coli full sequence array (EcFS) [EcFS_1, EcFS_2, and EcFS_3] |
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| Samples (90)
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| GSM1342339 |
OSU11, histidine depleted, 10 min, rep 1 |
| GSM1342340 |
OSU11, histidine depleted, 10 min, rep 2 |
| GSM1342341 |
OSU11, histidine depleted, 10 min, rep 3 |
| GSM1342342 |
OSU11, histidine depleted, 2 hrs, rep 1 |
| GSM1342343 |
OSU11, histidine depleted, 2 hrs, rep 2 |
| GSM1342344 |
OSU11, histidine depleted, 2 hrs, rep 3 |
| GSM1342345 |
OSU11, histidine depleted, >10 hrs, rep 1 |
| GSM1342346 |
OSU11, histidine depleted, >10 hrs, rep 2 |
| GSM1342347 |
OSU11, histidine depleted, >10 hrs, rep 3 |
| GSM1342348 |
OSU12-hisA, histidine supplied, 1 mM, rep 1 |
| GSM1342349 |
OSU12-hisA, histidine supplied, 1 mM, rep 2 |
| GSM1342350 |
OSU12-hisA, histidine supplied, 1 mM, rep 3 |
| GSM1342351 |
OSU12-hisA, histidine depleted, 10 min, rep 1 |
| GSM1342352 |
OSU12-hisA, histidine depleted, 10 min, rep 2 |
| GSM1342353 |
OSU12-hisA, histidine depleted, 10 min, rep 3 |
| GSM1342354 |
OSU12-hisA, histidine depleted, 2 hrs, rep 1 |
| GSM1342355 |
OSU12-hisA, histidine depleted, 2 hrs, rep 2 |
| GSM1342356 |
OSU12-hisA, histidine depleted, 2 hrs, rep 3 |
| GSM1342357 |
OSU12-hisA, histidine depleted, >10 hrs, rep 1 |
| GSM1342358 |
OSU12-hisA, histidine depleted, >10 hrs, rep 2 |
| GSM1342359 |
OSU12-hisA, histidine depleted, >10 hrs, rep 3 |
| GSM1342360 |
OSU12-hisB, histidine supplied, 1 mM, rep 1 |
| GSM1342361 |
OSU12-hisB, histidine supplied, 1 mM, rep 2 |
| GSM1342362 |
OSU12-hisB, histidine supplied, 1 mM, rep 3 |
| GSM1342363 |
OSU12-hisB, histidine depleted, 10 min, rep 1 |
| GSM1342364 |
OSU12-hisB, histidine depleted, 10 min, rep 2 |
| GSM1342365 |
OSU12-hisB, histidine depleted, 10 min, rep 3 |
| GSM1342366 |
OSU12-hisB, histidine depleted, 2 hrs, rep 1 |
| GSM1342367 |
OSU12-hisB, histidine depleted, 2 hrs, rep 2 |
| GSM1342368 |
OSU12-hisB, histidine depleted, 2 hrs, rep 3 |
| GSM1342369 |
OSU12-hisB, histidine depleted, >10 hrs, rep 1 |
| GSM1342370 |
OSU12-hisB, histidine depleted, >10 hrs, rep 2 |
| GSM1342371 |
OSU12-hisB, histidine depleted, >10 hrs, rep 3 |
| GSM1342372 |
OSU12-hisC, histidine supplied, 1 mM, rep 1 |
| GSM1342373 |
OSU12-hisC, histidine supplied, 1 mM, rep 2 |
| GSM1342374 |
OSU12-hisC, histidine supplied, 1 mM, rep 3 |
| GSM1342375 |
OSU12-hisC, histidine depleted, 10 min, rep 1 |
| GSM1342376 |
OSU12-hisC, histidine depleted, 10 min, rep 2 |
| GSM1342377 |
OSU12-hisC, histidine depleted, 10 min, rep 3 |
| GSM1342378 |
OSU12-hisC, histidine depleted, 2 hrs, rep 1 |
| GSM1342379 |
OSU12-hisC, histidine depleted, 2 hrs, rep 2 |
| GSM1342380 |
OSU12-hisC, histidine depleted, 2 hrs, rep 3 |
| GSM1342381 |
OSU12-hisC, histidine depleted, >10 hrs, rep 1 |
| GSM1342382 |
OSU12-hisC, histidine depleted, >10 hrs, rep 2 |
| GSM1342383 |
OSU12-hisC, histidine depleted, >10 hrs, rep 3 |
| GSM1342384 |
OSU12-hisD, histidine supplied, 1 mM, rep 1 |
| GSM1342385 |
OSU12-hisD, histidine supplied, 1 mM, rep 2 |
| GSM1342386 |
OSU12-hisD, histidine supplied, 1 mM, rep 3 |
| GSM1342387 |
OSU12-hisD, histidine depleted, 10 min, rep 1 |
| GSM1342388 |
OSU12-hisD, histidine depleted, 10 min, rep 2 |
| GSM1342389 |
OSU12-hisD, histidine depleted, 10 min, rep 3 |
| GSM1342390 |
OSU12-hisD, histidine depleted, 2 hrs, rep 1 |
| GSM1342391 |
OSU12-hisD, histidine depleted, 2 hrs, rep 2 |
| GSM1342392 |
OSU12-hisD, histidine depleted, 2 hrs, rep 3 |
| GSM1342393 |
OSU12-hisF, histidine supplied, 1 mM, rep 1 |
| GSM1342394 |
OSU12-hisF, histidine supplied, 1 mM, rep 2 |
| GSM1342395 |
OSU12-hisF, histidine supplied, 1 mM, rep 3 |
| GSM1342396 |
OSU12-hisF, histidine depleted, 10 min, rep 1 |
| GSM1342397 |
OSU12-hisF, histidine depleted, 10 min, rep 2 |
| GSM1342398 |
OSU12-hisF, histidine depleted, 10 min, rep 3 |
| GSM1342399 |
OSU12-hisF, histidine depleted, 2 hrs, rep 1 |
| GSM1342400 |
OSU12-hisF, histidine depleted, 2 hrs, rep 2 |
| GSM1342401 |
OSU12-hisF, histidine depleted, 2 hrs, rep 3 |
| GSM1342402 |
OSU12-hisF, histidine depleted, >10 hrs, rep 1 |
| GSM1342403 |
OSU12-hisF, histidine depleted, >10 hrs, rep 2 |
| GSM1342404 |
OSU12-hisF, histidine depleted, >10 hrs, rep 3 |
| GSM1342405 |
OSU12-hisG, histidine supplied, 1 mM, rep 1 |
| GSM1342406 |
OSU12-hisG, histidine supplied, 1 mM, rep 2 |
| GSM1342407 |
OSU12-hisG, histidine supplied, 1 mM, rep 3 |
| GSM1342408 |
OSU12-hisG, histidine depleted, 10 min, rep 1 |
| GSM1342409 |
OSU12-hisG, histidine depleted, 10 min, rep 2 |
| GSM1342410 |
OSU12-hisG, histidine depleted, 10 min, rep 3 |
| GSM1342411 |
OSU12-hisG, histidine depleted, 2 hrs, rep 1 |
| GSM1342412 |
OSU12-hisG, histidine depleted, 2 hrs, rep 2 |
| GSM1342413 |
OSU12-hisG, histidine depleted, 2 hrs, rep 3 |
| GSM1342414 |
OSU12-hisI, histidine supplied, 1 mM, rep 1 |
| GSM1342415 |
OSU12-hisI, histidine supplied, 1 mM, rep 2 |
| GSM1342416 |
OSU12-hisI, histidine supplied, 1 mM, rep 3 |
| GSM1342417 |
OSU12-hisI, histidine depleted, 10 min, rep 1 |
| GSM1342418 |
OSU12-hisI, histidine depleted, 10 min, rep 2 |
| GSM1342419 |
OSU12-hisI, histidine depleted, 10 min, rep 3 |
| GSM1342420 |
OSU12-hisI, histidine depleted, 2 hrs, rep 1 |
| GSM1342421 |
OSU12-hisI, histidine depleted, 2 hrs, rep 2 |
| GSM1342422 |
OSU12-hisI, histidine depleted, 2 hrs, rep 3 |
| GSM1342423 |
OSU12-hisI, histidine depleted, >10 hrs, rep 1 |
| GSM1342424 |
OSU12-hisI, histidine depleted, >10 hrs, rep 2 |
| GSM1342425 |
OSU12-hisI, histidine depleted, >10 hrs, rep 3 |
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| Relations |
| BioProject |
PRJNA240778 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE55719_RAW.tar |
3.7 Gb |
(http)(custom) |
TAR (of CEL) |
| GSE55719_normalized_data.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| Processed data are available on Series record |
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