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Status |
Public on Jan 05, 2018 |
Title |
DRUID: A pipeline for reproducible transcriptome-wide measurements of mRNA stability |
Organisms |
Saccharomyces cerevisiae; Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens; Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We present DRUID (for Determination of Rates Using Intron Dynamics), a computational pipeline, for determining mRNA stability transcriptome-wide uses metabolic labeling and approach-to-equilibrium kinetics. Our pipeline uses endogenous introns to normalize time course data and yields more reproducible half-lives than other methods, even with datasets that were otherwise unusable. DRUID can handle datasets from a variety of organisms, spanning yeast to humans.
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Overall design |
Transcription inhibition time courses (0, 1, 2, 4, 8, 12, 24 hr) using Actinomycin D or ⍺-amanitin were performed in HEK293 cells. Metabolic labeling time courses (1, 2, 4, 8, 12, 24 hr) using 4SU were performed in HEK293 and NIH3T3 cells. All experiments were performed in duplicate.
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Contributor(s) |
Lugowski A, Beth N, Rissland OS |
Citation(s) |
29438994 |
Submission date |
May 31, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Olivia Rissland |
E-mail(s) |
olivia.rissland@gmail.com
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Organization name |
The Hospital for Sick Children
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Street address |
686 Bay Street
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City |
Toronto |
ZIP/Postal code |
M5G 1X8 |
Country |
Canada |
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Platforms (4)
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GPL23529 |
Illumina HiSeq 2500 (Drosophila melanogaster; Homo sapiens; Saccharomyces cerevisiae) |
GPL23530 |
Illumina HiSeq 2500 (Caenorhabditis elegans; Drosophila melanogaster; Homo sapiens) |
GPL23531 |
Illumina HiSeq 2500 (Drosophila melanogaster; Mus musculus; Saccharomyces cerevisiae) |
GPL23532 |
Illumina HiSeq 2500 (Homo sapiens; Saccharomyces cerevisiae) |
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Samples (66)
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Relations |
BioProject |
PRJNA388686 |
SRA |
SRP108376 |
Supplementary file |
Size |
Download |
File type/resource |
GSE99517_ActD.HEK.HL.one.csv.gz |
981.2 Kb |
(ftp)(http) |
CSV |
GSE99517_ActD.HEK.HL.two.csv.gz |
912.2 Kb |
(ftp)(http) |
CSV |
GSE99517_Aman.HEK.HL.one.csv.gz |
898.6 Kb |
(ftp)(http) |
CSV |
GSE99517_Aman.HEK.HL.two.csv.gz |
918.3 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.DRUID.abnormalSpikeIns.csv.gz |
635.5 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.DRUID.notEnoughSpikeIns.csv.gz |
622.9 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.DRUID.one.csv.gz |
855.6 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.DRUID.two.csv.gz |
867.4 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.abnormalSpikeIns.csv.gz |
354.8 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.one.csv.gz |
864.1 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK.4SU.HL.two.csv.gz |
543.6 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.1.4SU.introns.preDRUID.csv.gz |
10.8 Mb |
(ftp)(http) |
CSV |
GSE99517_HEK293.2.4SU.introns.preDRUID.csv.gz |
12.2 Mb |
(ftp)(http) |
CSV |
GSE99517_HEK293.4SU.exon.csv.gz |
664.5 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.4SU.intron.csv.gz |
412.4 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.ActD.exon.csv.gz |
504.0 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.ActD.intron.csv.gz |
299.5 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.Aman.exon.csv.gz |
510.1 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.Aman.intron.csv.gz |
310.0 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.abnormalSpikeIns.4SU.exon.csv.gz |
426.7 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.abnormalSpikeIns.4SU.intron.csv.gz |
274.5 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.abnormalSpikeIns.4SU.introns.preDRUID.csv.gz |
11.4 Mb |
(ftp)(http) |
CSV |
GSE99517_HEK293.notEnoughSpikeins.4SU.exon.csv.gz |
462.0 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.notEnoughSpikeins.4SU.intron.csv.gz |
293.7 Kb |
(ftp)(http) |
CSV |
GSE99517_HEK293.notEnoughSpikeins.4SU.intron.preDRUID.csv.gz |
8.0 Mb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.1.4SU.introns.preDRUID.csv.gz |
10.1 Mb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.2.4SU.introns.preDRUID.csv.gz |
11.1 Mb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.HL.DRUID.one.csv.gz |
658.7 Kb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.HL.DRUID.two.csv.gz |
623.8 Kb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.HL.one.csv.gz |
643.9 Kb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.HL.two.csv.gz |
658.1 Kb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.exon.csv.gz |
623.4 Kb |
(ftp)(http) |
CSV |
GSE99517_NIH3T3.4SU.intron.csv.gz |
376.3 Kb |
(ftp)(http) |
CSV |
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