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Sample GSM3451719 Query DataSets for GSM3451719
Status Public on Jan 01, 2021
Title 256402110001_b1 - 1_1WT(4693)_S-_rep1 vs 5_1Mut(4693)_S-_rep1
Sample type RNA
 
Channel 1
Source name 5_1Mut_S-_rep1 allele 4693
Organism Pisum sativum
Characteristics tissue: cauline leaf
cultivar: cameor
genotype: PsSultr4 mutant
harvest date: 16-10-14
Treatment protocol Name:Sulfur deficiency - environmental treatment - sulfur concentration,sulfur:quantity 0mM .
Growth protocol caulin leaf - Media:Perlite (2/3) and sand B3 (1L pot) Temperature: 18 °C Light:16h/day
Extracted molecule total RNA
Extraction protocol 5_1Mut_S-:300mg. (Extraction_ARN_Trizol.doc)
Label Cy5
Label protocol labelling Cy3 and Cy5 direct, amplification=yes, total RNA .
 
Channel 2
Source name 1_1WT_S-_rep1 allele 4693
Organism Pisum sativum
Characteristics tissue: cauline leaf
cultivar: cameor
genotype: wildtype
harvest date: 16-10-14
Treatment protocol Name:Sulfur deficiency - environmental treatment - sulfur concentration,sulfur:quantity 0mM .
Growth protocol caulin leaf - Media:Perlite (2/3) and sand B3 (1L pot) Temperature: 18 °C Light:16h/day
Extracted molecule total RNA
Extraction protocol 1_1WT_S-:300mg. (Extraction_ARN_Trizol.doc)
Label Cy3
Label protocol labelling Cy3 and Cy5 direct, amplification=yes, total RNA .
 
 
Hybridization protocol 5_1Mut_S-_rep1 Cy5 / 1_1WT_S-_rep1 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.
Scan protocol GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%
Description Role of sulfur and of the sulfate store in leaf metabolism.
Data processing For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.
 
Submission date Oct 30, 2018
Last update date Jan 02, 2021
Contact name Stéphanie Pateyron
E-mail(s) pateyron@evry.inra.fr
Organization name IPS2_Institute of Plant Sciences Paris-Saclay
Lab Transcriptomic Plateforme POPS
Street address Rue de Noetzlin _ Batiment 630
City Orsay
ZIP/Postal code 91405
Country France
 
Platform ID GPL25688
Series (1)
GSE121967 Transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase

Data table header descriptions
ID_REF ID number
VALUE Normalized log2 ratio median intensity of Ch1(Cy5)/Ch2(Cy3) (Ch2=reference)

Data table
ID_REF VALUE
CD859581 0.290333296591498
CD859582 -0.245799134196623
CD859679 -0.0705276256926082
CD859707 -0.0213139092227004
CD859745 -3.5749711173755
CD859827 0.612489386132601
CD859854 -0.0519372328147149
CD859868 -0.104832132815472
CD859877 -0.0450453393964147
CD859898 -0.187804795618345
CD859906 1.63305649596502
CD859936 0.00462895487090109
CD859966 0.384001769919385
CD860127 0.0548387390914756
CD860128 -0.333617669022665
CL10Contig1 0.108898597957372
CL11Contig1 0.0344278734114084
CL12Contig1 0.244154896596034
CL13Contig1 -0.89866990300557
CL14Contig1 0.00969601943530152

Total number of rows: 40777

Table truncated, full table size 1225 Kbytes.




Supplementary file Size Download File type/resource
GSM3451719_256402110001_b1.gpr.gz 21.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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