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Sample GSM6726739 Query DataSets for GSM6726739
Status Public on Nov 15, 2023
Title WholeRoot_625µMP_6d_rep1 [sP6d.1]
Sample type RNA
 
Source name Whole root, 625 µM P, 6 days, replicate 1
Organism Arabidopsis thaliana
Characteristics tissue: whole root
treatment: 625 µM P
time after treatment: 6 days
Treatment protocol Seven-day-old seedlings precultured on sufficient phosphorus were transferred to fresh solid half-strength Murashige and Skoog medium containing 625 µM KH2PO4 (sufficient P) or 100 µM KH2PO4 (deficient P). The missing potassium in the P-deficient medium was supplied as KCl.
Growth protocol Seeds of Arabidopsis thaliana (Columbia-0, CS60000) were surface sterilized in 70% (v/v) ethanol and 0.05% (v/v) Triton X-100. Seedlings were first germinated for seven days on agar plates containing 0.5% (w/v) sucrose and 1% (w/v) agar before seedlings of similar sizes were transferred to treatments containing identical sucrose and agar concentrations. The nutrient composition was half-strenght Murashige and Skoog and Difco agar (Becton Dickinson; cat. number 214541;) was used as gelling agent. In the preculture, 625 µM P was supplied as KH2PO4. In treatment plates, the solid half-strength MS medium contained 625 µM P (sufficient P) or 100 µM P (deficient P), with 525 µM K being supplied as KCl. Each treatment plate contained 10 seven-day-old seedling. Each replicate was composed of 5 plates containing 10 seven-day-old seedling each (i.e., 50 plants pooled as one replicate). Agar plates were sealed with Leukopor tape (Smith & Nephew) and placed vertically in a randomized block design within a growth cabinet (Percival Scientific) with 22°C day and 19°C night temperatures and a 10-h light period with a light intensity of 120 µmol photons m-2 s-1.
Extracted molecule total RNA
Extraction protocol RNA was extracted from whole roots (roots of 50 plants pooled togeher to form one replicate) using an RNeasy plant mini kit (Qiagen) with on-column DNase treatment according to the manufacturer’s instructions. cDNA was prepared using random hexamer primers and SuperScript II reverse transcriptase (Life Technologies) according to the manufacturer’s protocol.
Label Cy3
Label protocol RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).
 
Hybridization protocol RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.
Description Gene expression after 6 days of 625 µM posphate treatment
Data processing The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 021169_D_F_20140929) to obtain background subtracted and spatially detrended Processed Signal intensities. Analysis of microarray data was performed with the R package limma. Raw feature intensities were background corrected using “normexp”, and “quantile” normalization method was used to normalize between arrays.
 
Submission date Nov 11, 2022
Last update date Nov 15, 2023
Contact name Anja Hartmann
E-mail(s) hartmann@ipk-gatersleben.de
Phone +49 39482 5-578
Organization name IPK Gatersleben
Department PZB
Lab MPE
Street address Corrensstraße 3
City Seeland
State/province Saxony-Anhalt
ZIP/Postal code 06466
Country Germany
 
Platform ID GPL12621
Series (1)
GSE217790 Expression signatures of Arabidopsis thaliana roots under low or high phosphate conditions.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_84_P10000 3.764918451
A_84_P10001 5.289478948
A_84_P10002 8.824484981
A_84_P10004 2.787555331
A_84_P10005 10.51143851
A_84_P100056 11.25615543
A_84_P10006 3.921220062
A_84_P10007 11.13240255
A_84_P10008 9.338683134
A_84_P10009 2.787555331
A_84_P10010 7.52607671
A_84_P10011 4.417489452
A_84_P10012 3.585712975
A_84_P10013 5.393324982
A_84_P10014 3.109584657
A_84_P10015 13.77758036
A_84_P100156 3.764918451
A_84_P10016 6.430788443
A_84_P10017 9.043151846
A_84_P10018 3.109584657

Total number of rows: 35334

Table truncated, full table size 846 Kbytes.




Supplementary file Size Download File type/resource
GSM6726739_US91603673_252116914669_S01_GE1_1105_Oct12_1_2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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