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Series GSE115428 Query DataSets for GSE115428
Status Public on Jun 06, 2021
Title Global transcriptomic response to chilling temperature in Col-0 wild type and sig5-3 (SALK_141383C) mutant Arabidopsis plants.
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Investigate whether a nuclear-encoded sigma factor (SIGMA FACTOR5, SIG5; controls chloroplast transcription) regulates the transcriptome (RNA-seq) in response to chilling.
Overall design Col-0 wild type and sig5-3 seedlings were grown under light/dark cycles for 11 days and exposed to continuous light for 24 h before start of experiment. After 24 h under continuous light, one set of seedlings was exposed to 5 h chilling (4 °C), commencing at ZT27, and the other set was exposed to 3 h of chilling, commencing at ZT45. Both sets of chilled samples had parallel controls that were not chilled (19 °C). Each treatment had 3 independent replicates. Total RNA was extracted and RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA kit. Sequencing was performed using an Illumina NextSeq 500 using NSQ 500 Hi-Output kit v2 (150 cycle). Sequence data were imported into Partek Genomics Suite version 6.6 (Partek, St. Louis, 385 MO, USA), further trimmed and aligned to the Arabidopsis thaliana genome (TAIR11) using STAR (version 2.4.1d). Genes with a fold change of |log2| > 1.5 and a false detection rate of < 0.05 were considered as differentially-expressed.
Contributor(s) Cano-Ramirez D, Dodd AN
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Submission date Jun 06, 2018
Last update date Jun 06, 2021
Contact name Antony N Dodd
Phone +44 (0) 117 39 41176
Organization name University of Bristol
Department Life Sciences Building
Street address 24 Tyndall Avenue
City Bristol
ZIP/Postal code BS8 1TQ
Country United Kingdom
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (24)
GSM3178066 Col-0 19C ZT27 rep1
GSM3178067 Col-0 19C ZT27 rep2
GSM3178068 Col-0 19C ZT27 rep3
BioProject PRJNA474938
SRA SRP149937

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Supplementary file Size Download File type/resource
GSE115428_DLCRAND_gene_counts.txt.gz 1.6 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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