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Series GSE99517 Query DataSets for GSE99517
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
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.
 
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.
 
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
Organization name The Hospital for Sick Children
Street address 686 Bay Street
City Toronto
ZIP/Postal code M5G 1X8
Country Canada
 
Platforms (4)
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)
Samples (66)
GSM2645366 293_1_4SU_1h_R1.fastq.gz
GSM2645367 293_1_4SU_2h_R1.fastq.gz
GSM2645368 293_1_4SU_4h_R1.fastq.gz
Relations
BioProject PRJNA388686
SRA SRP108376

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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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Raw data are available in SRA
Processed data are available on Series record

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