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Sample GSM4196701 Query DataSets for GSM4196701
Status Public on May 31, 2020
Title siz_SIM4d_r1
Sample type SRA
 
Source name Excised hypocotyl from dark-grown seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia (Col-0)
genotype: siz1-2
time of sampling: After CIM 4 days and SIM 4 days
Treatment protocol Hypocotyl explants (around 10mm long) were excised using a razor blade and incubated on CIM (Gamborg B5 medium with 0.25% Gelzan supplemented with 0.5 μg/ml 2,4-dichlorophenoxyacetic acid [2,4-D] and 0.05 μg/ml kinetin) for 4 days under constant light. Hypocotyl or root explants were then transferred to SIM (Gamborg B5 medium 0.25% Gelzan, 0.15ug/ml IAA and 0.5 ug/ml 2-IPA)
Growth protocol 22°C constant temperature in the dark vertically grown on 1%Sucrose 1X MS medium containing 0.6% Gelzan CM growth 7 days
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-seq for siz1-2 hypocotyl explant incubated on CIM 4d and SIM4d replicate 1
Data processing Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 1.2.1 with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Comma-delimited data with transcript CPM (counts per million mapped reads) values for each sample
 
Submission date Nov 29, 2019
Last update date Jun 01, 2020
Contact name Duncan Peter Coleman
Organization name Riken
Department CSRS
Lab Cell Function Research
Street address 1-7-22 Suehiro-cho, Tsurumi-ku
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL19580
Series (1)
GSE141188 Gene expression profile of Arabidopsis thaliana wild type and siz1-2 mutant during in vitro shoot regeneration on callus inducing media (CIM) and shoot inducing media (SIM)
Relations
BioSample SAMN13429496
SRA SRX7241982

Supplementary file Size Download File type/resource
GSM4196701_siz1_2_SIM4d_r1.csv.gz 249.4 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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