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Sample GSM3178086 Query DataSets for GSM3178086
Status Public on Jun 06, 2021
Title Col-0 4C ZT45 rep 3
Sample type SRA
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics temperature: 4C
time in ll (zt): 45
genotype: wild type
Treatment protocol 24 hours under constant light and then exposed to 19 °C or 4 °C starting at two different times of day (ZT 27 and ZT 45).
Growth protocol 11 days 12 h photoperiod 19°C
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from three samples of 10 seedlings each, using Macherey-Nagel Nucleospin II RNA extraction kits.
RNA sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA kit, according to manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description DR-48-C3_R1_val
Data processing Base calling by RTA 2.4.6 and FASTQ creator by BaseSpace.
Sequence data were trimmed for adaptor sequence and imported into Partek Genomics Suite version 6.6
Sequenced reads were mapped to TAIR11 using STAR - 2.5.3a
Quantification to annotated model was performed using Quantify to annotation model (Partek E/M) for strict paired-end settings.
Counts were normalized using the TMM with defaulst settings. Means <= 1.0 were excluded.
Genome_build: TAIR 11
Supplementary_files_format_and_content: tab-delimited text file with locus ID and counts per sample (columns)
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
Platform ID GPL19580
Series (1)
GSE115428 Global transcriptomic response to chilling temperature in Col-0 wild type and sig5-3 (SALK_141383C) mutant Arabidopsis plants.
BioSample SAMN09375744
SRA SRX4178381

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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