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Sample GSM4974265

Query DataSets for GSM4974265

Status

Public on Oct 28, 2021

Title

PminusFeminus39hours1

Sample type

SRA

Source name

7 day old shoots

Organism

Arabidopsis thaliana

Characteristics

background ecotype: Col-0
treatment: -P-Fe
time: 39h after transfer
tissue: shoots

Treatment protocol

Arabidopsis wild-type plants (Col-0 accession) were grown on control (+Fe+P) for 7 days on 0.1X MS then transferred to three different medium: control (+Fe+P), iron deficiency (-Fe+P), and iron and phosphate deficiency conditions (-Fe-P). Shoots were collected 39 h, 52 h and 76 h after the transfer. For RNA-seq experiments, three biological replicates were used for each time point (39h, 52h and 76h) and each condition (+Fe+P, -Fe+P and -Fe-P) for a total of 27 samples.

Extracted molecule

polyA RNA

Extraction protocol

RNeasy Plant Mini Kit (QIAGEN)
KAPA Biosystems RNA HyperPrep Kit

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Reads were mapped with HISAT2 to the Arabidopsis thaliana TAIR10 reference genome using the Galaxy (Version 2.1.0+galaxy5) web platform.
The resulting BAM files were then analyzed on R using the DESeq2 and TxDB.Athaliana.BioMart.plantsmart28 (Bioconductor) packages. Genes with padj<0.05 were considered differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel

Submission date

Dec 14, 2020

Last update date

Oct 28, 2021

Contact name

Yanniv Dorone

Organization name

Stanford University

Street address

371 Jane Stanford Way

City

Stanford