NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3762843 Query DataSets for GSM3762843
Status Public on Nov 01, 2019
Title 5Pi_cZ_R2
Sample type SRA
 
Source name roots
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
treatment: grown without phosphate and treated with cis-zeatin
Growth protocol Arabidopsis thalinaan (Col-0) seedlings were grown in Murashige and Skoog medium containing 625 or 5 µM of phosphate for 8 days and then treated with 5 µM of cis-zeatin or trans-zeatin fro 8 hours.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary
polyA library
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description grown without phosphate and treated with cis-zeatin
Data processing Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014). Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference genome (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: FDR<0.05, fold change >2 fold or < -2 fold
Genome_build: Atabidopsis thaliannTAIR 10
Supplementary_files_format_and_content: tab-delimited text files including normalized counts.
 
Submission date May 11, 2019
Last update date Nov 01, 2019
Contact name Juan Carlos del Pozo
E-mail(s) pozo@inia.es
Organization name Centro de Biotecnología y Genómica de Plantas
Department Biotechnology
Lab 180
Street address Campus de Montegancedo, UPM
City Pozuelo de Alracon
State/province Madrid
ZIP/Postal code 28223
Country Spain
 
Platform ID GPL13222
Series (1)
GSE131056 Role of cis-zeatin in root responses to phosphate starvation
Relations
BioSample SAMN11625713
SRA SRX5822290

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap