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Sample GSM1049877 Query DataSets for GSM1049877
Status Public on Apr 05, 2013
Title AC_T_rep1
Sample type RNA
 
Source name tomato fruit_turning/breaker
Organism Solanum lycopersicum
Characteristics variety: Ailsa Craig
tissue: ripening tomato fruit
ripening stage: turning/breaker (T)
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 04_AC_T_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 3.963508002
Solyc00g005040 3.899056441
Solyc00g005050 217.0181974
Solyc00g005100 37.13582941
Solyc00g005110 3.824894989
Solyc00g005150 5.565637431
Solyc00g005440 3.920326313
Solyc00g005450 4.965291718
Solyc00g005460 10.56650506
Solyc00g005470 3.569895889
Solyc00g005480 4.626117158
Solyc00g005840 30.23126646
Solyc00g006480 4.244141112
Solyc00g006490 139.0920826
Solyc00g006500 8.265407237
Solyc00g006510 8.265801991
Solyc00g006520 9.733619619
Solyc00g006530 9.033967151
Solyc00g006540 8.062003642
Solyc00g006550 4.141235396

Total number of rows: 28672

Table truncated, full table size 752 Kbytes.




Supplementary file Size Download File type/resource
GSM1049877_A246_04_AC_T_1_EUTOM3_exon_.CEL.gz 7.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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