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Sample GSM3936261 Query DataSets for GSM3936261
Status Public on Dec 02, 2019
Title 4.5µM NAA rep1
Sample type SRA
 
Source name rosette
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
tissue: rosette
genotype: wild type
age: 15-day old
Growth protocol Seeds were germinated on Gamborg's B5 media (Phytotechnoloy Laboratory, USA) for 12 days after which they were transferred to control (0.1% EtOH), melatonin (5 or 100µM) or NAA(4.5µM) supplemented Gamborg's B5 media for 3 days. Growth conditions of the controlled environment room were 23°C, 56% relative humidity (RH), Light intensity 120 μmol m-2 s-1, photoperiod: 16h/8h light/dark cycle
Extracted molecule total RNA
Extraction protocol Rosettes were carefully separated from roots, immediately flash frozen in liquid nitrogen and stored at -80°C until further analysis. RNA was harvested using Spectrum™ Plant Total RNA kit (STRN250,Sigma, NSW, Australia) following manufacturer’s guidelines. Illumina TruSeq stranded mRNA library kit (Catalog # RS-122-9004) was used for construction of sequencing libraries.
Libraries were prepared using standard protocol by TruSeq stranded mRNA library kit (Illumina, Catalog # RS-122-9004)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing bcl2fastq2 Conversion Software v2.20 was used to convert bcl to fastq files and remove adapter sequences
Read quality control was conducted by using the FastQC software (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The Kallisto program (Bray et al., 2016) was used to determine transcript abundance as transcripts per million (TPM) by pseudoalignment of reads to the Araport11 model transcriptome with a k-mer length of 31 (Cheng et al., 2017).
For differential gene expression analysis, the sleuth program was used which utilizes a Wald test to determine differential gene expression (Pimentel et al., 2017).
Genes with a false discovery rate (FDR) of < 0.05 and log2 fold change of at least 1.2 were classified as differentially expressed.
For functional analysis, gene ontology (GO) term enrichment of differentially expressed genes was conducted from a publicly available database (www.geneontology.org) and functional GO annotations for each gene was obtained from the bulk data retrieval tool in TAIR (www.arabidopsis.org).
Genome_build: pseudoalignment of reads to the Araport11 model transcriptome (www.arabport.org) with a k-mer length of 31 (Cheng et al., 2017).
Supplementary_files_format_and_content: The processed data files contains the TPM values for each gene across samples from the kallisto output
 
Submission date Jul 10, 2019
Last update date Dec 02, 2019
Contact name Sajal Fatima Zia
E-mail(s) S.Zia@latrobe.edu.au
Organization name La Trobe University
Department Animal, Plant and Soil Sciences
Lab Kim Plummer
Street address Agribio, 5 Ring Rd, Bundoora VIC 3083
City Melbourne
State/province VIC
ZIP/Postal code 3083
Country Australia
 
Platform ID GPL19580
Series (1)
GSE134079 Comparative transcriptome analysis of melatonin or auxin treated-Arabidopsis
Relations
BioSample SAMN12248632
SRA SRX6426840

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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