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Sample GSM5359146 Query DataSets for GSM5359146
Status Public on Feb 15, 2022
Title Col_17C_SIM4D_rep1
Sample type SRA
Source name Hypocotyl explant
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
treatment: 4 days on CIM then 4 days on SIM
temperature: 17°C
replicate: 1
tissue: Hypocotyl explant
Treatment protocol Explants were first incubated on CIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 7.5 g.L-1 Gellan gum, 0.1 mg.L-1 kinetin and 0.5 mg.L-1 2,4 D, for 4 days in continuous light conditions and at 17°C or 27°C. Explants were then transferred on SIM, i.e. MS medium supplemented with Gamborg’s B5 vitamin, 20 g.L-1 glucose, 0.5 g.L-1 MES, 2.5 g.L-1 Gellan gum, 0.5 mg.L-1 2-iP and 0.15 mg.L-1 IAA, for 4 days in continuous light conditions and at 17°C or 27°C.
Growth protocol Plants were grown on nylon mesh over MS medium containing 1% sucrose and 0.6% (w/v) gelzan. Plates were placed vertically and kept in the dark at 22°C to induce hypocotyl elongation. 7-day-old etiolated seedlings were dissected with a razor blade to harvest hypocotyls explants located between ~3 mm above the root/hypocotyl junction and ~5 mm below the hypocotyl/shoot junction.
Extracted molecule total RNA
Extraction protocol ~100 hypocotyls explants harvested and frozen with liquid nitrogen. The samples were then ground using zirconia ceramic beads in a TissueLyser (QIAGEN) mixer mill. RNA was extracted using the RNeasy Plant Mini kit (QIAGEN) following the manufacturer's instructions.
Libraries for sequencing were prepared using the KAPA Stranded mRNA-seq Kit (Kapa Biosystems, Roche) with a mix of FastGene (Nippon Genetics) and NEBNext (New England Biolabs) adapters.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Sequencing quality was first checked using FastQC (version 0.11.7).
Reads were then mapped to the TAIR10 Arabidopsis genome using Bowtie2 (version with the "--no-1mm-upfront" option.
Resulting SAM files were converted to BAM using the samtools (version 1.9) function "view".
Duplicated reads were removed with samtools "rmdup".
Resulting BAM files were sorted and indexed with samtools "sort" and "index".
Read counts per gene were determined using the "multicov" function from bedtools (version 2.26.0) and were used to produce the Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed file.
Genome_build: TAIR10
Supplementary_files_format_and_content: Coverage_all_17C_VS_27C_CIM_SIM_RNA-seq.bed is a tab-delimited BED (~.txt) file containing the read counts for each TAIR10 genes in each sequencing sample.
Submission date Jun 04, 2021
Last update date Feb 15, 2022
Contact name Alice Lambolez
Organization name The University of Tokyo
Department Faculty of Science, Department of Biological Sciences
Lab Kakutani Lab
Street address 7 Chome-3-1 Hongo
City Bunkyo
State/province Tokyo
ZIP/Postal code 113-8654
Country Japan
Platform ID GPL19580
Series (1)
GSE176161 Gene expression during hormone-induced shoot regeneration in Arabidopsis thaliana explants exposed to different temperatures
BioSample SAMN19572117
SRA SRX11068486

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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