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Sample GSM255011 Query DataSets for GSM255011
Status Public on Jan 15, 2008
Title WT Rice branching panicle vs. dsRNAiRFL Sample B_SWAP
Sample type RNA
 
Channel 1
Source name WT rice TP309 branching panicles
Organism Oryza sativa
Characteristics Rice TP309; wild type branching panicles
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from WT rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.
Label Cy5
Label protocol cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy3 labeled cRNA synthesis using T7 dependent in vitro transcription system.
 
Channel 2
Source name Transgenic rice panicles knock down for RFL
Organism Oryza sativa
Characteristics Transgenic rice branching panicles of similar developmental stage to WT where a transcription regulator, RFL has been knocked down by double stranded RNA interference
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from RFL knock down rice panicles using Tri Reagent (Sigma) and purified by RNeasy cleanup kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.
Label Cy3
Label protocol cDNA was synthesized from tortal RNA by RT-PCR and was used as templete for Cy5 labeled cRNA synthesis using T7 dependent in vitro transcription system.
 
 
Hybridization protocol Probe fragmentation: Fragmentation reaction was as-
cRNA Cy3 750 ng,cRNA Cy5 750 ng,Blocking agent 50 ul,Water variable, 25 X fragmentation buffer,10 ul to 250 ul total volume.
Incubate at 60C for 30 mins. Add 250 ul of 2X hybridization buffer.
Use 490 ul for each slide and hybridize at 65C for 17 hrs at 5 rpm speed.
Scan protocol Washing was done according to Agilent’s instructions using wash buffer 1 followed by wash buffer 2. Slides were scanned using Agilent DNA Microarray Scanner (G2565BA).
Description Image quality was checked with the help of-
1. Four green spots and each corner of the image
2. SpikeIn A and B control spots across the image
3. Evenness of the background in log-scale mode
Data processing The TIFF image was used to extract raw and processed data using Agilent’s Feature Extraction software (FE v8.1). The normalization was done using GeneSpring GX version 7.2 using the recommended Per Spot and Per Chip: Intensity dependent (Lowess) normalization. Number of non-control spots with ratio 0.25 and below were considered as down regulated spots.
 
Submission date Jan 08, 2008
Last update date Jan 23, 2008
Contact name Nagashree N Rao
E-mail(s) nagashri@mcbl.iisc.ernet.in
Phone 91-80-22932681
Fax 91-80-23600168
URL http://mcbl.iisc.ernet.in
Organization name Indian Institute of Science
Department Microbiology and Cell Biology
Lab Prof. Usha Vijayraghavan
Street address C.V. Raman Avenue
City Bangalore
State/province Karnataka
ZIP/Postal code 560012
Country India
 
Platform ID GPL892
Series (1)
GSE10098 Identification of downstream genes regulated by RFL

Data table header descriptions
ID_REF
VALUE log2 ratio of test/wild-type
CH1 Cy3 signal intensity
CH2 Cy5 signal intensity
PRE_VALUE ratio of CH1 (Cy5) vs CH2 (Cy3)
INV_VALUE log2 of PRE_VALUE

Data table
ID_REF VALUE CH1 CH2 PRE_VALUE INV_VALUE
1 -0.0466 3005.83 2910.3042 1.0328233 0.0466
2 0.3413 41.0709 52.03361 0.7893148 -0.3413
3 0.0305 826.332 844.0114 0.9790531 -0.0305
4
5
6 -0.3573 5986.69 4673.2793 1.2810469 0.3573
7 0.1319 1868.16 2047.0146 0.9126266 -0.1319
8 2.1471 576.802 2554.873 0.22576544 -2.1471
9
10 0.1936 1256.32 1436.7446 0.8744212 -0.1936
11
12
13 0.7271 98.783 163.51242 0.60413146 -0.7271
14 -0.1088 372.935 345.85397 1.0783019 0.1088
15 -0.2177 1898.48 1632.5452 1.1628958 0.2177
16
17
18 -0.0597 220.024 211.10524 1.0422479 0.0597
19 -0.371 1159.29 896.4043 1.2932669 0.3710
20 0.6324 17.5299 27.174519 0.64508593 -0.6324

Total number of rows: 21495

Table truncated, full table size 876 Kbytes.




Supplementary file Size Download File type/resource
GSM255011.txt.gz 5.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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