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Sample GSM146729 Query DataSets for GSM146729
Status Public on Nov 28, 2006
Title Head Short Day Cy5 Rep3
Sample type RNA
 
Channel 1
Source name Head of pea aphid reared under 16h photoperiod: reference channel
Organism Acyrthosiphon pisum
Characteristics Strain: YR2 (red holocyclic clone)
Parthenogenetic female
10 days of 16h photoperiod
Instar stage L3
Female producing parthenogenetic females
Biomaterial provider INRA Rennes, UMR 1099 BiO3P
Treatment protocol Long Day reared pea aphids
Growth protocol The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 16 h of light (“long-day” or LD) that maintained parthenogenesis. To initiate the experiment clonal third instar larvae (L3) were placed under LD photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood (wingless adults or WA) and produced offspring (G1) that were transferred onto new plants and kept under LD conditions. A batch of 50 L3-G1 aphids was collected in the middle of the photophase (15:00) and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of asexual forms in LD.
Extracted molecule total RNA
Extraction protocol RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). This Channel 1 sample corresponds to a mixture of total RNAs taken from the three replicated samples reared under Long Day photoperiod. RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).
Label Cy3
Label protocol 5 µg of aRNA were labelled and purified using the CyScribe Post-labelling (anchored oligo-dT primed) and the CyScribe GFX Purification kits (Amersham Biosciences-GE, Fairfield, CT, USA)
 
Channel 2
Source name Head of pea aphid reared under 12h photoperiod
Organism Acyrthosiphon pisum
Characteristics Strain: YR2 (red holocyclic clone)
Parthenogenetic female
10 days of 12h photoperiod
Instar stage L3
Parthenogenetic female producing sexual individuals
Biomaterial provider INRA Rennes, UMR 1099 BiO3P
Treatment protocol Short Day reared pea aphids
Growth protocol The clone YR2 of the pea aphid A. pisum was reared on broad bean (Vicia fabae) at 18°C. Parthenogenetic reproduction was maintained at 16 h of light and aphids were reared at low density (one to five individuals per plant) over three generations to prevent the production of winged forms. Conditions: 12 h of light (“short-day” or SD) that induced sexual forms after two generations. To initiate the experiment clonal third instar larvae (L3) were placed at SD photoperiod. This corresponds to generation G0. L3-G0 aphids reached adulthood (wingless adults or WA) and produced offspring (G1) that were transferred onto new plants and kept under SD conditions. A batch of 50 L3-G1 aphids was collected in the middle of the photophase (15:00) and immediately frozen in liquid nitrogen. As a control, few G1 aphids were maintained on plants to confirm the production of sexual forms in SD.
Extracted molecule total RNA
Extraction protocol RNAs were extracted from heads using either the RNeasy Mini kit (Qiagen, Germantown, MD, USA). RNAs were amplified by using MessageAmp aRNA kit (Ambion, Austin, TX, USA), starting with 2 µg of total RNA. RNAs were checked with a Bioanalyzer 2100 (Agilent Tech. Inc., Palo Alto, CA, USA), and quantified with a Nanodrop (Agilent).
Label Cy5
Label protocol 5 µg of aRNA were labelled and purified using the CyScribe Post-labelling (anchored oligo-dT primed) and the CyScribe GFX Purification kits (Amersham Biosciences-GE, Fairfield, CT, USA).
 
 
Hybridization protocol Hybridizations were performed in a Discovery XT System hybridization robot using the ChipMap 80 kit (Ventana Medical Systems, Tucson, AZ, USA) at the OUEST-Genopole and Agenae transcriptomic facilities (INRA Sribe, Rennes, France). Prehybridization was performed at 42ºC for 1 h in 2 ml of ChipSpread buffer containing 4xSSC and 0.2% SDS. Target cDNAs were mixed before hybridizations at 42ºC for 6 h (protocol N°2, ALC-D60/10-H48/8, Ventana). Washes were performed manually at room temperature in 1xSSC.
Scan protocol Fluorescent images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v5.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA, USA).
Description none
Data processing Raw data were normalized by the MADSCAN software. After subtraction of the fluorescence background, a rank-invariant method and a spatial normalisation were performed before a scaling of the variance within each slide and between all the slides at the same rank. The normalized values were log-transformed and used to perform statistical analysis by GeneANOVA. The contribution of each experimental factor (Gene, Photoperiod, Biological replicate, Dye, Technical replicate) and the interaction between them was evaluated by a global ANOVA. Differentially expressed genes where selected by imposing stringent cut-offs on the local ANOVA graphic of the interaction “Gene-Photoperiod”
 
Submission date Nov 22, 2006
Last update date Nov 27, 2006
Contact name Denis TAGU
E-mail(s) denis.tagu@rennes.inra.fr
Organization name INRA Rennes
Department UMR 1099 BiO3P
Street address BP35327
City Le Rheu
ZIP/Postal code BP35653
Country France
 
Platform ID GPL4580
Series (1)
GSE6363 Effect of day-length shortening on gene expression on pea aphid heads

Data table header descriptions
ID_REF
VALUE Log2(Gnorm/Rnorm)
Rmed Median of Cy3 fluorescence
Rbmed Background - median of Cy3 fluorescence
Gmed Median of Cy5 fluorescence
Gbmed Background of Cy5 fluorescence
Rnorm Normalisation of Rmed
Gnorm Normalisation of Gmed
A coefficient of variation: (Log2Rnorm+Log2Gnorm)/2

Data table
ID_REF VALUE Rmed Rbmed Gmed Gbmed Rnorm Gnorm A
1a -0.01 2565 54 3548 178 2906 2927 11.51
2a 1.45 1610 55 345 171 858 314 9.02
3a 0.1 1238 52 572 174 709 662 9.42
4a 1.73 2616 54 683 181 2069 624 10.15
5a -1.15 1874 52 5316 183 2055 4561 11.58
6a 0.64 4342 52 5068 187 5713 3666 12.16
7a 0.73 4703 56 5294 189 6273 3782 12.25
8a 1.38 2009 56 537 186 1333 512 9.69
9a 0.8 1692 58 595 169 1097 630 9.7
10a -0.63 127 54 244 172 58 90 6.18
11a 0.54 4951 56 6400 173 6654 4576 12.43
12a 1.38 1891 54 474 177 1193 458 9.53
13a 1.06 1698 55 497 180 1046 501 9.5
14a -0.15 1445 53 1012 174 1028 1140 10.08
15a -0.1 1430 55 940 172 996 1067 10.01
16a 0.08 1239 54 584 180 709 671 9.43
17a -1 801 52 579 169 391 781 9.11
18a -0.03 3809 52 6912 180 4991 5095 12.3
19a 0.66 2052 52 1072 177 1687 1067 10.39
20a 0.56 2264 52 1514 174 2091 1418 10.75

Total number of rows: 6720

Table truncated, full table size 271 Kbytes.




Supplementary data files not provided

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