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Sample GSM2560252 Query DataSets for GSM2560252
Status Public on Jun 01, 2017
Title Control rep3
Sample type SRA
 
Source name Control_root
Organism Arabidopsis thaliana
Characteristics strain: Col-0
genotype/variation: wild type
age: 3 days after germination
tissue: root
treated with: none (control)
Treatment protocol Three days after germination (dag), seedlings were incubated in liquid 1/2 MS and 1/2 MS supplemented with 1 µM IAA for 6 h.
Growth protocol Arabidopsis Col-0 seeds were surface-sterilized and vernalized for 7 days at 4°C. Seedlings were grown vertically at 22°C and 150 µmol m-2 s -1 under a 16-h light/8-h dark cycle on 1/2 Murashige and Skoog (MS) media (Sigma).
Extracted molecule total RNA
Extraction protocol Roots were collected in liquid nitrogen. Each replicate contained approximately 100 roots. Total RNA from the roots was extracted using TRIzol® Reagent (Ambion, Cat. Num. 15596-018) and DNaseI (Promega), and total RNA yields were measured using an Invitrogen® Qubit™ fluorometer and Agilent Bioanalyzer 2100 microfluidics (Agilent, Santa Clara, CA). Complementary DNA was synthesized using a Revert Aid First Strand cDNA Synthesis Kit (Thermo SCIENTIFIC, USA).
Ribosomal RNA depletion was performed using a RiboMinus™ Plant Kit for RNA-Seq (Invitrogen™), according to the manufacturer’s instructions. Five micrograms of RNA with an RNA integrity number (RIN) of 7.9-9.0 was used. Three hundred nanograms of ribo-depleted RNA was taken for SOLiD cDNA barcoded fragment library construction using a SOLiD™ Total RNA-Seq Kit (Applied Biosystems™). cDNA libraries were amplified by PCR with 16 cycles following the recommendations of the sample preparation protocol. Library concentrations and quality were assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA) and had an average length of ~250 bp. e-PCR (emulsion quantitative polymerase reaction) was performed with a library concentration of 60 pmol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Data processing Raw reads were mapped onto the Arabidopsis genome (TAIR10) using SHRiMP (v2.2.3)
Uniquely mapped reads were counted using the htseq-count program with the annotation file from TAIR10
The DEGs were detected using the Bioconductor package DESeq
Genome_build: TAIR10
 
Submission date Mar 31, 2017
Last update date May 15, 2019
Contact name Daniil Wiebe
E-mail(s) daniil.wiebe@gmail.com
Organization name ICG SBRAS
Street address Lavrentyeva 10
City Novosibirsk
ZIP/Postal code 630090
Country Russia
 
Platform ID GPL16033
Series (1)
GSE97258 Auxin regulates functional gene groups in a fold-specific manner in Arabidopsis root
Relations
BioSample SAMN06670795
SRA SRX2693029

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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