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Sample GSM2088160 Query DataSets for GSM2088160
Status Public on Jun 12, 2017
Title OsHOX24-overexpression seedlings, drought stress, rep2
Sample type RNA
Source name Rice seedlings
Organism Oryza sativa
Characteristics genotype/variation: OsHOX24 overexpressed
stress: drought
ecotype: Pusa Basmati 1
tissue: Seedlings
age: Three week old
Treatment protocol For control conditions and drought stress treatment, seedlings were kept in RO water and dried between folds of tissue paper at 28 ┬▒ 1 degree celsius for 3 h, respectively
Growth protocol Wild-type and transgenic rice seedlings were grown in hydroponics system (trays) containing Yoshida medium, at 28┬▒1 degree celsius for three weeks, in a culture room with a daily photoperiodic cycle of 14 h light and 10 h dark
Extracted molecule total RNA
Extraction protocol Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions
Label Biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® 3' IVT PLUS Reagent Kit User Manual, Affymetrix)
Hybridization protocol Following fragmentation, 3.5 ug of labelled 2nd cycle ss-cDNA were hybridized for 17 h at 45 degree celsius on GeneChip whole target expression array. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 as per FS450_0002 fluidics protocol.
Scan protocol GeneChips were scanned using GeneChip Scanner 3000
Description Gene expression data from drought stress treated OsHOX24 overexpression rice seedlings
Data processing CEL files were imported into Genespring software and probe summarization and normalization was performed using RMA algorithm
Submission date Mar 14, 2016
Last update date Jun 12, 2017
Contact name Mukesh Jain
Phone 91-11-26704686
Organization name Jawaharlal Nehru University
Street address New Mehrauli Road
City New Delhi
State/province New Delhi
ZIP/Postal code 110067
Country India
Platform ID GPL21593
Series (1)
GSE79212 Gene expression analysis in wild-type and OsHOX24 rice overexpression line under control and drought stress conditions

Data table header descriptions
VALUE RMA signal intensity

Data table
16027395 2.9500175
15980936 7.413912
16059629 9.056114
15850572 3.3490496
15970290 1.2512563
15959972 5.668516
15913337 6.827354
15914210 3.2443457
15983178 1.2610295
15844012 8.513586
15985552 5.1712103
15921900 8.884782
15877036 7.532548
15862066 2.3169332
15892360 6.2214317
16038173 3.9649045
15799599 6.5757546
16052501 3.206067
16042312 7.60202
15940731 1.8646375

Total number of rows: 54922

Table truncated, full table size 996 Kbytes.

Supplementary file Size Download File type/resource
GSM2088160_HB1_DS_rep2.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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