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Sample GSM1049880 Query DataSets for GSM1049880
Status Public on Apr 05, 2013
Title AC_RR_rep1
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 07_AC_RR_1
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
E-mail(s) ruud.demaagd@wur.nl
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
ID_REF
VALUE RMA normalized expression values are reported for each sample and replicate

Data table
ID_REF VALUE
Solyc00g005000 4.012654762
Solyc00g005040 4.558018662
Solyc00g005050 179.258243
Solyc00g005100 23.1609184
Solyc00g005110 4.238123316
Solyc00g005150 6.979324365
Solyc00g005440 5.166986554
Solyc00g005450 7.549601994
Solyc00g005460 7.815623012
Solyc00g005470 3.333834431
Solyc00g005480 4.871432417
Solyc00g005840 9.338403096
Solyc00g006480 4.151634708
Solyc00g006490 103.0577794
Solyc00g006500 16.33390825
Solyc00g006510 5.818402795
Solyc00g006520 13.4790961
Solyc00g006530 13.97562295
Solyc00g006540 9.194711545
Solyc00g006550 4.310118467

Total number of rows: 28672

Table truncated, full table size 752 Kbytes.




Supplementary file Size Download File type/resource
GSM1049880_A246_07_AC_R_1_EUTOM3_exon_.CEL.gz 7.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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