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Sample GSM3164880 Query DataSets for GSM3164880
Status Public on May 31, 2018
Title Harumi_30_DAF
Sample type RNA
Source name Harumi, 30 day after flowering, polyembryonic
Organism (Citrus unshiu x Citrus sinensis) x Citrus reticulata
Characteristics cultivar: Harumi
tissue: whole young fruit
embryonic: polyembryonic
Treatment protocol Whole young fruits at 15, 30, 45 and 60 DAF were collected for microarray analysis, immediately frozen in liquid nitrogen, and stored at −80°C for RNA isolation.
Growth protocol ‘Kiyomi’ and ‘Harumi’, cultivated at NARO Institute of Fruit and Tea Tree Science (NIFTS), Department of Citrus Research (Shizuoka, Japan), were used as materials for monoembryonic and polyembryonic varieties, respectively.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted following Ikoma et al. (1996) J. Jpn. Soc. Hort. Sci. 64: 809-814.
Label Cy3
Label protocol RNA samples were labelled with cyanine-3-labelled cytosine triphosphate using a Low Input Quick-Amp Labelling Kit (Agilent Technologies) according to the manufacturer’s directions.
Hybridization protocol The labelled cRNAs were subsequently hybridized on the custom oligo-DNA microarray using a Gene Expression Hybridization kit (Agilent Technologies) according to the manufacturer’s directions.
Scan protocol After washing in GE washing buffer (Agilent Technologies), the glass slides were scanned with an Agilent Microarray Scanner (G2505C, Agilent Technologies).
Description Gene expression 30 day after flowering in whole young fruit of polyembryonic citrus cultivar 'Harumi'
Data processing The Feature Extraction software (version, employing defaults for all parameters, was used to convert the images into gene expression data.
Submission date May 30, 2018
Last update date May 31, 2018
Contact name Hiroshi Fujii
Organization name Institute of Fruit Tree Science, NARO
Department Division of Citrus Research
Street address 485-6 Okitsunakacho, Shimizu
City Shizuoka
State/province Shizuoka
ZIP/Postal code 424-0292
Country Japan
Platform ID GPL25057
Series (1)
GSE115082 MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

Data table header descriptions
VALUE The raw data were normalized to the 75th percentile intensity of probes, log transformation base 2, centering by mean.

Data table
C22975 -0.67689896
Cle-07408-CD13A 0.047397494
Cle-07408-CD13S -0.32852817
Cle-07408-CD16A -0.5512976
C06501 -0.5517137
Cle-07408-CD16S 0.063970566
C06502 0.10472965
C06500 0.40265012
C06505 0.21227121
C06506 -1.5989735
C06503 -0.416794
C06504 0.5951027
C06509 -0.2582531
C06507 0.444968
C06508 0.49770403
Cle-07408-CD15A -0.5482483
C06520 1.413954
C06512 -0.43712473
C06513 -0.4262517
Cle-07408-CD15S -0.3326869

Total number of rows: 30884

Table truncated, full table size 564 Kbytes.

Supplementary file Size Download File type/resource
GSM3164880_US82800151_257910710001_S01_GE1_107_Sep09_2_2.txt.gz 8.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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