NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM934755 Query DataSets for GSM934755
Status Public on May 22, 2012
Title LS_001_bA
Sample type RNA
 
Source name WT, Col-0 16°C, LL, whole inflorescences, replicate A
Organism Arabidopsis thaliana
Characteristics cultivar: Col-0
Treatment protocol none.
Growth protocol Plants were grown on soil at 16°C and LL until flowering.
Extracted molecule total RNA
Extraction protocol For synthesis of targets, 1 µg of total RNA was used as template for generation of cRNA using the MessageAmp II-Biotin Enhanced Kit (Ambion, Austin, TX, USA). We followed the manufacturer’s instruction with one exception: For tiling arrays, biotinylated NTPs were replaced by unmodified NTPs (stock solution 25 mM each).7 µg unmodified cRNA (for tiling arrays) was converted into dsDNA (GeneChip® WT Double-Stranded cDNA Synthesis Kit, Affymetrix, Santa Clara, CA, USA) and dsDNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, Hilden, Germany).
Label biotin
Label protocol 7.5 µg dsDNA was fragmented and labeled using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Probes were hybridized to Arabidopsis Tiling 1.0R arrays for 14 h at 42°C. Arrays were washed using a Fluidics Station 450, wash protocol FS450_0001.
Scan protocol Tiling arrays were scanned using a GeneChip® Scanner 3000 7G.
Data processing All probes that were not identically conserved in the genomes of Col-0, Bur-0 and C24 were excluded. If less than three conserved probes composed a probe set the complete set was completely excluded. For expression measurements for probe set definitions RMA normalization was applied (see Laubinger et al., Genome Biol. 2008, and Zeller et al., Plant J., 2009, for details)
 
Submission date May 22, 2012
Last update date May 22, 2012
Contact name Felix Ott
Organization name Max Planck Institute for Developmental Biology
Street address Spemannstr. 35-39
City Tuebingen
ZIP/Postal code 72076
Country Germany
 
Platform ID GPL10977
Series (2)
GSE38109 Natural variation in Arabidopsis thaliana transcriptomes
GSE38113 Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

Supplementary file Size Download File type/resource
GSM934755_LS_001_bA_R_A.CEL.gz 24.1 Mb (ftp)(http) CEL
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap