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Sample GSM1261970 Query DataSets for GSM1261970
Status Public on Jan 01, 2015
Title Leaf-ZH2_spring_rep2
Sample type RNA
 
Source name fresh shoots, Zhonghuang 2, replicate 2
Organism Camellia sinensis
Characteristics tissue: fresh shoots (two and a bud)
sampling season: spring
Treatment protocol In the spring, the fresh shoots (two and a bud) were sampled from the four cultivars.
Growth protocol Four tea plant cultivars, "Longjing 43", "Zhongcha 108", "Zhonghuang 1" and "Zhonghuang 2" were grown in the China National Germplasm Hangzhou Tea Repository (CNGHTR) at the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS).
Extracted molecule total RNA
Extraction protocol RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Hybridization protocol 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the Camellia sinensis 44K custom array (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting.
Description Gene expression in spring
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as "Detected" were maintained.
 
Submission date Nov 11, 2013
Last update date Jan 01, 2015
Contact name Lu Wang
E-mail(s) wanglu317@tricaas.com
Organization name Tea Research Institute, Chinese Academy of Agricultural Sciences
Street address 9th, South Meiling Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310008
Country China
 
Platform ID GPL17911
Series (1)
GSE52255 Development of a 44K custom oligo microarray using 454 pyrosequencing data for large scale gene expression analysis in tea plant (Camellia sinensis)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 11.385663
DarkCorner 2.0756555
CUST_5902_PI428262022 9.480429
CUST_8443_PI428262022 11.982959
CUST_29704_PI428262014 10.77569
CUST_12442_PI428262014 7.143087
CUST_50480_PI428262022 12.540805
CUST_24260_PI428262014 8.658996
CUST_17732_PI428262014 14.421702
CUST_12474_PI428262022 4.270442
CUST_10342_PI428262014 2.7323055
CUST_8653_PI428262022 6.286852
CUST_10637_PI428262014 2.877716
CUST_12512_PI428262022 4.941012
CUST_12751_PI428262022 5.308579
CUST_6922_PI428262014 3.8628852
CUST_21239_PI428262022 12.265835
CUST_57210_PI428262014 2.5339835
CUST_23371_PI428262014 2.104293
CUST_11079_PI428262014 8.026383

Total number of rows: 42500

Table truncated, full table size 1336 Kbytes.




Supplementary file Size Download File type/resource
GSM1261970_Zhonghuang_2-2.txt.gz 6.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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