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Sample GSM1382317 Query DataSets for GSM1382317
Status Public on Jan 11, 2015
Title 1FLC/SVP._SD.Apex.r3
Sample type RNA
 
Source name FLC+/SVP+ 2 weeks Short Days - ZT8-Apex
Organism Arabidopsis thaliana
Characteristics developmental stage: 2 weeks old short days
treatment: additional 2 short 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 3.477783285
AT1G01020_at 5.294884351
AT1G01030_at 3.812560611
AT1G01040_at 3.532273085
AT1G01046_at 3.013983617
AT1G01050_at 9.147645356
AT1G01060_at 3.173597745
AT1G01070_at 6.344398481
AT1G01080_at 7.894700914
AT1G01090_at 10.52286895
AT1G01100_at 11.30045857
AT1G01110_at 4.900716806
AT1G01115_at 4.000508212
AT1G01120_at 6.224337334
AT1G01130_at 5.898849892
AT1G01140_at 5.203263503
AT1G01150_at 2.989702995
AT1G01160_at 8.452951674
AT1G01170_at 9.662533553
AT1G01180_at 5.165641702

Total number of rows: 31004

Table truncated, full table size 753 Kbytes.




Supplementary file Size Download File type/resource
GSM1382317_33_2011_Atdschip_tiling.CEL.gz 19.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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