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Sample GSM2396841 Query DataSets for GSM2396841
Status Public on Aug 22, 2017
Title Col-0 +Pi
Sample type SRA
Source name Root apex (2-3 mm)
Organism Arabidopsis thaliana
Characteristics ecotype: Col 0 (CS70000)
genotype: wild type
phosphate treatment: High Phosphate
duration of treatment: 5 days after germination
tissue: root tips (2-3 mm from the root apex)
Treatment protocol Treatmens included Low Phosphate and Low Iron (Iron as FeSO4 was not added to the medium solution and 100 µM ferrozine (C20H12N4Na2O6S2; SIGMA) were added to chelate any Fe traces) and Malate Supplementation (-Pi medium supplemented with 1 mM L-malate (SIGMA) prior to pH adjustment).
Growth protocol Briefly, seeds were grown 5 days after germination under high phosphate(1mM Pi, +Pi) or low phosphate (5µM, -Pi) conditions in petri dishes with 0.1X Modified MS media (1% w/v Sucrose, pH 5.7, and 1% w/v agar).
Extracted molecule total RNA
Extraction protocol For RNA-Seq total RNA was isolated using the TRIZOL reagent (Invitrogen) according to the manufacturer's instructions.
For preparation of mRNA-Seq Libraries, total RNA was isolated from frozen root tip powder using the TRIzol® reagent (Invitrogen) according to the manufacturer’s instructions for isolation of total RNA from plant tissue. Non–strand-specific mRNA-seq libraries were generated from 5 μg of total RNA (Plant RNeasy kit) and prepared by using the TruSeq RNA Sample Prep kit (Illumina) according to the manufacturer’s instructions.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Basecalls for RNA-Seq were performed using illumina basecalling pipeline (SolexaPipeline 1.0). ShortRNA-Seq reads with 75-nt reads from each end generated by Illumina sequencing were aligned to the Arabidopsis thaliana reference genome reference genome sequences were downloaded from TAIR.
Alignment of RNA-Seq reads was performed using TopHat2. Count of RNA-Seq reads was performed using HTSeq-count.
Genome_build: TAIR 10
Supplementary_files_format_and_content: The count file has two columns that provide ID (Arabidopsis locus ID) and read number (the number of reads that were alligned to that locus).
Submission date Nov 18, 2016
Last update date May 15, 2019
Contact name Luis Rafael Herrera-Estrella
Organization name Cinvestav - Langebio
Department Langebio
Lab Plant Physiology and Metabolic Engineering
Street address Km 9.6 Libramiento Norte Carretera León
City Irapuato
State/province Guanajuato
ZIP/Postal code 36821
Country Mexico
Platform ID GPL19580
Series (1)
GSE90061 Whole genome RNA-sequencing from root tips ofArabidopsis thalianalow-phosphate insensitive mutants under High and Low phosphate
BioSample SAMN06040779
SRA SRX2360456

Supplementary file Size Download File type/resource
GSM2396841_col0hp.count.txt.gz 128.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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