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Sample GSM2688424 Query DataSets for GSM2688424
Status Public on Jul 01, 2018
Title T4hSub_1
Sample type RNA
 
Source name Intercalary meristem at the 10~12 weeks stem in 4h Submergence, non-transgenic
Organism Oryza sativa
Characteristics cultivar: cv. Pin Gaew 56 (PG56)
stress: Submergence
time: 4h
tissue: intercalary meristem
Treatment protocol Deepwater rice stem sections were pre-incubated for 4 h and then further incubated complete submergence or air in continuous light for 24 h. Twenty stem sections were placed in an upright position in a 200-ml glass beaker which was then filled with glass beads to prevent the submerged sections from floating up. Each beaker containing the sections was lowered to the bottom of a plastic cylinder, filled to the 50-cm deep with distilled water. Stem sections were incubated under complete submergence or in air for 3 different times (0, 1 and 4 h).
Growth protocol Seeds (Oriza sativa L. indica cultivar Pin Gaew 56) were geminated in darkness in petri dishes on moist filter paper at 30℃ for 72 h. Seedling were transplanted in plastic pots and grown in greenhouse. Twenty-cm-long stem sections containing the uppermost internode were excised from 10- to 12-week-old plants.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using MiniBEST Plant RNA Extraction kit (TAKARA, Japan).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description Intercalary meristem at the 10~12 weeks stem in 4h Submergence, non-transgenic, biological replicate 1
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Jun 28, 2017
Last update date Jul 01, 2018
Contact name Yeon-Ki Kim
E-mail(s) kim750a11@gmail.com
Phone 82-31-321-6351
Organization name GreenGene Biotech Inc.
Department GreenGene Biotech Inc.
Lab Genomics & Genetics Ins.
Street address 38-2 Namdong
City Yongin
State/province Kyonggido
ZIP/Postal code 449-728
Country South Korea
 
Platform ID GPL14568
Series (1)
GSE100598 Transcriptome analysis of early submergence-responsive genes in deepwater rice

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
Os03g0388900 385.086
Os09g0502900 164.382
Os08g0511900 5338.68
Os05g0457200 601.286
Os04g0643200 3159.39
Os12g0221400 224.585
Os04g0499300 3524.24
Os11g0592400 690.241
Os06g0186500 203.809
Os02g0503100 41.7574
Os05g0130100 221.191
Os02g0187100 425.022
Os05g0196100 954.503
Os01g0628700 152.451
Os05g0490800 2046.32
Os04g0137500 3030.8
Os01g0195400 1887.42
Os06g0141000 972.545
Os03g0805600 165.333
Os06g0259000 110.8

Total number of rows: 31588

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM2688424_T4hSub1_362336A10_102909_532.probe.gz 1.9 Mb (ftp)(http) PROBE
GSM2688424_T4hSub1_532_nm_norm_RMA.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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