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| Status |
Public on Jan 01, 2019 |
| Title |
Global RNA half lives in cyanobacteria |
| Organism |
Picosynechococcus sp. PCC 7002 |
| Experiment type |
Other
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| Summary |
We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.
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| Overall design |
Samples were taken from three replicates of WT PCC 7002 (labeled 2,3,and 4). Samples taken before the addition of rifampicin were called '0 minutes' and labeled with 'A'. Subsequent timepoints (0.5 minutes, 1 minute, 2.5 minutes, 5 minutes, 7.5 minutes, and 10 minutes) were labeled respectively B, C, D, E, F, and G. Three replicates were taken with 7 timepoints each leading to 21 samples total.
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| Contributor(s) |
Gordon GC, Cameron JC, Pfleger BF |
| Citation(s) |
32753502 |
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| Submission date |
Jan 13, 2018 |
| Last update date |
Aug 24, 2020 |
| Contact name |
Gina Gordon |
| E-mail(s) |
[email protected]
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| Organization name |
University of Wisconsin Madison
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| Department |
Chemical and Biological Engineering
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| Lab |
Brian Pfleger Laboratory
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| Street address |
1415 Engineering Dr
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platforms (1) |
| GPL21381 |
Illumina HiSeq 2500 (Synechococcus sp. PCC 7002) |
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| Samples (21)
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| GSM2934745 |
2D: replicate A, 2.5 minutes |
| GSM2934746 |
2E: replicate A, 5 minutes |
| GSM2934747 |
2F: replicate A, 7.5 minutes |
| GSM2934748 |
2G: replicate A, 10 minutes |
| GSM2934749 |
3A: replicate B, 0 minutes |
| GSM2934750 |
3B: replicate B, 0.5 minutes |
| GSM2934751 |
3C: replicate B, 1 minute |
| GSM2934752 |
3D: replicate B, 2.5 minutes |
| GSM2934753 |
3E: replicate B, 5 minutes |
| GSM2934754 |
3F: replicate B, 7.5 minutes |
| GSM2934755 |
3G: replicate B, 10 minutes |
| GSM2934756 |
4A: replicate C, 0 minutes |
| GSM2934757 |
4B: replicate C, 0.5 minutes |
| GSM2934758 |
4C: replicate C, 1 minute |
| GSM2934759 |
4D: replicate C, 2.5 minutes |
| GSM2934760 |
4E: replicate C, 5 minutes |
| GSM2934761 |
4F: replicate C, 7.5 minutes |
| GSM2934762 |
4G: replicate C, 10 minutes |
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| Relations |
| BioProject |
PRJNA429921 |
| SRA |
SRP130967 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE109174_Gene_counts_and_half_lives.xlsx |
1.0 Mb |
(ftp)(http) |
XLSX |
| GSE109174_RAW.tar |
49.3 Mb |
(http)(custom) |
TAR (of CSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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