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Sample GSM1049881 Query DataSets for GSM1049881
Status Public on Apr 05, 2013
Title AC_RR_rep2
Sample type RNA
Source name tomato fruit_red ripe
Organism Solanum lycopersicum
Characteristics variety: Ailsa Craig
tissue: ripening tomato fruit
ripening stage: red ripe (RR)
Treatment protocol Fruits kept at -80C untill further use, and ground in liquied nitrogen before RNA extraction
Growth protocol Tomato plants were grown in a greenhouse on rockwool with liquied nutrient solution
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using an InviTrap Spin Plant RNA mini kit (Stratec, Berlin)
Label biotin
Label protocol RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands. corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0). For array analysis, total RNA (100 ng) was used for whole transcript cDNA synthesis using the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands), and subsequently labeled using the Affymetrix GeneChip WT Terminal Labeling Kit [catalog number 901524] (Affymetrix, Santa Clara, CA).
Hybridization protocol Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45C in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).
Scan protocol Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).
Description 08_AC_RR_2
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).
Submission date Dec 06, 2012
Last update date Apr 05, 2013
Contact name Ruud A de Maagd
Organization name Plant Resarch International
Street address PO Box 619
City Wageningen
ZIP/Postal code NL-6700AP
Country Netherlands
Platform ID GPL16358
Series (2)
GSE42783 Gene expression in three stages of ripening tomato fruit
GSE42784 Comparison of tomato fruit gene expression data obtained by microarray analysis and by treatment of degradome sequencing data as an RNAseq experiment

Data table header descriptions
VALUE RMA normalized expression values are reported for each sample and replicate

Data table
Solyc00g005000 4.203322553
Solyc00g005040 3.242445267
Solyc00g005050 185.0599111
Solyc00g005100 10.13140601
Solyc00g005110 4.222310376
Solyc00g005150 3.686433743
Solyc00g005440 3.507100258
Solyc00g005450 6.341833279
Solyc00g005460 12.75161374
Solyc00g005470 3.396437453
Solyc00g005480 4.05000953
Solyc00g005840 21.0790659
Solyc00g006480 4.122205331
Solyc00g006490 122.9993921
Solyc00g006500 7.895326143
Solyc00g006510 7.670767256
Solyc00g006520 19.87164531
Solyc00g006530 7.711814132
Solyc00g006540 4.432932135
Solyc00g006550 3.483664595

Total number of rows: 28672

Table truncated, full table size 752 Kbytes.

Supplementary file Size Download File type/resource
GSM1049881_A246_08_AC_R_2_EUTOM3_exon_.CEL.gz 7.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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