|
| 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 |
|
| Relations |
| BioSample |
SAMN06040779 |
| SRA |
SRX2360456 |
