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| Status |
Public on Dec 16, 2017 |
| Title |
Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq] |
| Organism |
Synechococcus elongatus PCC 7942 = FACHB-805 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions
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| Overall design |
Cyanobacteria were grown under either a Low Light, Clear Day, High Light pulse, or Shade pulse condition, and gene expression was measured periodically using RNA sequencing
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| Contributor(s) |
Piechura JR, Amarnath K, O'Shea EK |
| Citation(s) |
29239721 |
| Submission date |
Sep 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Joseph Robert Piechura |
| E-mail(s) |
jpiechura25@gmail.com
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| Organization name |
Harvard University
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| Department |
FAS Center for Systems Biology
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| Lab |
Erin O'Shea Lab
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| Street address |
52 Oxford Street
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platforms (1) |
| GPL17750 |
Illumina HiSeq 2500 (Synechococcus elongatus PCC 7942) |
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| Samples (60)
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| GSM2792387 |
Low Light, 0.5 hours since dawn, replicate 1 |
| GSM2792388 |
Low Light, 0.5 hours since dawn, replicate 2 |
| GSM2792389 |
Low Light, 2 hours since dawn, replicate 1 |
| GSM2792390 |
Low Light, 2 hours since dawn, replicate 2 |
| GSM2792391 |
Low Light, 4 hours since dawn, replicate 1 |
| GSM2792392 |
Low Light, 4 hours since dawn, replicate 2 |
| GSM2792393 |
Low Light, 6 hours since dawn, replicate 1 |
| GSM2792394 |
Low Light, 6 hours since dawn, replicate 2 |
| GSM2792395 |
Low Light, 8 hours since dawn, replicate 1 |
| GSM2792396 |
Low Light, 8 hours since dawn, replicate 2 |
| GSM2792397 |
Low Light, 9 hours since dawn, replicate 1 |
| GSM2792398 |
Low Light, 9 hours since dawn, replicate 2 |
| GSM2792399 |
Low Light, 10 hours since dawn, replicate 1 |
| GSM2792400 |
Low Light, 10 hours since dawn, replicate 2 |
| GSM2792401 |
Low Light, 12 hours since dawn, replicate 1 |
| GSM2792402 |
Low Light, 12 hours since dawn, replicate 2 |
| GSM2792403 |
Clear Day, 0.5 hours since dawn, replicate 1 |
| GSM2792404 |
Clear Day, 0.5 hours since dawn, replicate 2 |
| GSM2792405 |
Clear Day, 2 hours since dawn, replicate 1 |
| GSM2792406 |
Clear Day, 2 hours since dawn, replicate 2 |
| GSM2792407 |
Clear Day, 4 hours since dawn, replicate 1 |
| GSM2792408 |
Clear Day, 4 hours since dawn, replicate 2 |
| GSM2792409 |
Clear Day, 6 hours since dawn, replicate 1 |
| GSM2792410 |
Clear Day, 6 hours since dawn, replicate 2 |
| GSM2792411 |
Clear Day, 8 hours since dawn, replicate 1 |
| GSM2792412 |
Clear Day, 8 hours since dawn, replicate 2 |
| GSM2792413 |
Clear Day, 9 hours since dawn, replicate 1 |
| GSM2792414 |
Clear Day, 9 hours since dawn, replicate 2 |
| GSM2792415 |
Clear Day, 10 hours since dawn, replicate 1 |
| GSM2792416 |
Clear Day, 10 hours since dawn, replicate 2 |
| GSM2792417 |
Clear Day, 12 hours since dawn, replicate 1 |
| GSM2792418 |
Clear Day, 12 hours since dawn, replicate 2 |
| GSM2792419 |
High Light Pulse, 8 hours since Dawn, Time 0, replicate 1 |
| GSM2792420 |
High Light Pulse, 8 hours since Dawn, Time 0, replicate 2 |
| GSM2792421 |
High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1 |
| GSM2792422 |
High Light Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2 |
| GSM2792423 |
High Light Pulse, 8.5 hours since Dawn, Time 30 min, replicate 1 |
| GSM2792424 |
High Light Pulse, 8.5 hours since Dawn, Time 30 min, replicate 2 |
| GSM2792425 |
High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 1 |
| GSM2792426 |
High Light Pulse, 9 hours since Dawn, Time 60 min, replicate 2 |
| GSM2792427 |
High Light Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 1 |
| GSM2792428 |
High Light Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 2 |
| GSM2792429 |
High Light Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 1 |
| GSM2792430 |
High Light Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 2 |
| GSM2792431 |
High Light Pulse, 10 hours since Dawn, Time 60 min return, replicate 1 |
| GSM2792432 |
High Light Pulse, 10 hours since Dawn, Time 60 min return, replicate 2 |
| GSM2792433 |
Shade Pulse, 8 hours since Dawn, Time 0, replicate 1 |
| GSM2792434 |
Shade Pulse, 8 hours since Dawn, Time 0, replicate 2 |
| GSM2792435 |
Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 1 |
| GSM2792436 |
Shade Pulse, 8.25 hours since Dawn, Time 15 min, replicate 2 |
| GSM2792437 |
Shade Pulse, 8.5 hours since Dawn, Time 30 min, replicate 1 |
| GSM2792438 |
Shade Pulse, 8.5 hours since Dawn, Time 30 min, replicate 2 |
| GSM2792439 |
Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 1 |
| GSM2792440 |
Shade Pulse, 9 hours since Dawn, Time 60 min, replicate 2 |
| GSM2792441 |
Shade Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 1 |
| GSM2792442 |
Shade Pulse, 9.25 hours since Dawn, Time 15 min return, replicate 2 |
| GSM2792443 |
Shade Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 1 |
| GSM2792444 |
Shade Pulse, 9.5 hours since Dawn, Time 30 min return, replicate 2 |
| GSM2792445 |
Shade Pulse, 10 hours since Dawn, Time 60 min return, replicate 1 |
| GSM2792446 |
Shade Pulse, 10 hours since Dawn, Time 60 min return, replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE104204 |
Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions |
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| Relations |
| BioProject |
PRJNA412032 |
| SRA |
SRP118803 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE104203_Natural_light_RNAseq_processed.xlsx |
4.6 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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