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Sample GSM1382332 Query DataSets for GSM1382332
Status Public on Jan 11, 2015
Title 4flc/svp.LD.Apex.r3
Sample type RNA
 
Source name flc-/svp- 2 weeks Short Days + 2 Long days-ZT8-Apex
Organism Arabidopsis thaliana
Characteristics developmental stage: 2 weeks old short days
treatment: additional 2 long days
tissue: Apex
cultivar: Columbia
Treatment protocol Plants were collected either after two weeks growing in short days or transfered to two days to long days. All genotypes were collected at ZT8.
Growth protocol Plants were grown on soil in short days at 22°C.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNA Plant Mini kit, QIAGEN from leaves and apices.
Label biotin
Label protocol Total RNA samples (150 ng) were reverse transcribed into double-stranded cDNA and then in vitro transcribed in the presence of biotin-labeled nucleotides using the GeneChip 3′ IVT Express kit (Affymetrix; 901229) including poly(A) controls as recommended by the manufacturer. The quality and quantity of the biotinylated cRNA were determined using NanoDrop ND 1000 and Bioanalyzer 2100. Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35 min. at 94°C in fragmentation buffer (Affymetrix).
 
Hybridization protocol Biotinylated cRNA samples were mixed in 250 μL of Hybridization Mix (Affymetrix; 900720) containing Hybridization Controls and Control Oligonucleotide B2 (Affymetrix; 900454). Samples were hybridized onto Affymetrix AGRONOMICS1 Arabidopsis tiling arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 using the FS450_0004 protocol.
Scan protocol An Affymetrix GeneChip Scanner 3000 was used to measure the fluorescence intensity emitted by the labeled target.
Data processing The raw data (CEL files) were subjected to RMA.
 
Submission date May 07, 2014
Last update date Jan 11, 2015
Contact name Julieta Mateos
E-mail(s) jmateos@leloir.org.ar
Phone +054 11 5238-7500
Organization name Max Planck Institute for Plant Breeding Research
Department Department of Plant Developmental Biology
Lab Control of Flowering Time
Street address Carl-von-Linné-Weg 10
City Cologne
ZIP/Postal code D-50829
Country Germany
 
Platform ID GPL18660
Series (1)
GSE57416 Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AT1G01010_at 3.522461051
AT1G01020_at 5.314751712
AT1G01030_at 3.68486082
AT1G01040_at 3.583171984
AT1G01046_at 2.91100729
AT1G01050_at 9.251224657
AT1G01060_at 3.417739037
AT1G01070_at 6.809850813
AT1G01080_at 8.075479299
AT1G01090_at 10.64620171
AT1G01100_at 11.51955915
AT1G01110_at 5.116781378
AT1G01115_at 3.486200137
AT1G01120_at 5.874080356
AT1G01130_at 6.198315913
AT1G01140_at 5.756767742
AT1G01150_at 3.203319203
AT1G01160_at 8.505233497
AT1G01170_at 9.148913238
AT1G01180_at 5.43427979

Total number of rows: 31004

Table truncated, full table size 753 Kbytes.




Supplementary file Size Download File type/resource
GSM1382332_48_2011_Atdschip_tiling.CEL.gz 19.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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