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Sample GSM3579961 Query DataSets for GSM3579961
Status Public on Jan 26, 2019
Title HS_SC_PA1: psp1 mutant rep1
Sample type SRA
 
Source name Aerial part
Organism Arabidopsis thaliana
Characteristics tissue: Aerial part
ecotype: Columbia
genotype/variation: psp1 mutant
Treatment protocol Three independent biological replicates of aerial part and roots of each sample were harvested at the end of the night period for the analysis
Growth protocol Wild type and psp1 mutant plants were sterilized and sown on 0.8% agar plates containing one-fifth-strength Murashige and Skoog medium with Gamborg vitamins, buffered with 0.9 g/l MES (adjusted to pH 5.7 with Tris). After four days of stratification at 4°C, plates were vertically placed in a growth chamber at 20-22ºC under a 16 h day/8 h night photoperiod, 100 μmol m−2 s−1.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using NucleoSpin RNA II kit (Macherey-Nagel)
Using 3-15 μg of RNA as starting material, a mRNA enrichment was performed with the MicroPoly(A) Purist kit (AMBION). To prepare the RNA-Seq library, the SOLID Total RNA-seq kit (Life Technologies) was used. After obtaining the library, an equimolar mixture of it was used to perform an emulsion PCR using the automatic system of EZ Beads (Life Technologies). Then, the bead enrichment was performed, followed by its deposition in the sequencing wells. The sequencing step was performed using a SOLID 5500XL equipment of 75 nucleotides using the Exact Call Chemistry. Single end reads in fastq format were mapped against the TAIR10 Arabidopsis transcriptome (www.arabidopsis.org) using kallisto (v0.43.0 with default parameters except l=200 and s=30), (Bray et al., 2016). Data was combined in R (v3.3.2) and analyzed. Principal component analysis was carried out with prcomp (scale=T). Differential expression was assessed with edgeR in classic mode (Robinson et al., 2010) followed by Benjamini Hochberg correction (Benjamini and Hochberg, 1995). Enrichment analysis were conducted using topGO (R package version 2.22.0) with Fisher’s Exact Test (Fisher, 1922) followed by Benjamini Yekutieli correction (Benjamini and Yekutieli, 2001). The level of significance was fixed at 0.01 (1%) after correction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB 5500xl Genetic Analyzer
 
Description phosphoserine phosphatase mutant
Data processing Single end reads in fastq format were mapped against the TAIR10 Arabidopsis transcriptome (www.arabidopsis.org) using kallisto (v0.43.0 with default parameters except l=200 and s=30), (Bray et al., 2016
Data was combined in R (v3.3.2) and analyzed
Principal component analysis was carried out with prcomp (scale=T).
Differential expression was assessed with edgeR in classic mode (Robinson et al., 2010) followed by Benjamini Hochberg correction (Benjamini and Hochberg, 1995).
Enrichment analysis were conducted using topGO (R package version 2.22.0) with Fisher’s Exact Test (Fisher, 1922) followed by Benjamini Yekutieli correction (Benjamini and Yekutieli, 2001).
 
Submission date Jan 25, 2019
Last update date Jan 26, 2019
Contact name Roc Ros
E-mail(s) roc.ros@uv.es
Organization name Universitat de Valencia
Department Biologia Vegetal
Street address Vicent Andres Estelles
City Burjassot
State/province valencia
ZIP/Postal code 46100
Country Spain
 
Platform ID GPL16033
Series (1)
GSE125675 Deficiency in the Phosphorylated Pathway of Serine Biosynthesis perturbs sulfur assimilation in Arabidopsis
Relations
BioSample SAMN10820220
SRA SRX5293409

Supplementary file Size Download File type/resource
GSM3579961_HS_SC_PA1.abundance.tsv.gz 294.5 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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