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Sample GSM1123061 Query DataSets for GSM1123061
Status Public on Apr 15, 2018
Title Sample2_exp2_chip1_rep2
Sample type RNA
 
Channel 1
Source name Late male embryos; 18-28 hours post laying; 140-500 individuals per replicate
Organism Nasonia vitripennis
Characteristics Sex: male
developmental stage: late embryos
tissue: whole body
strain: AsymCX
Treatment protocol Samples were prepared at 25º C as follows: Approximately 200 N. vitrirpennis (AsymCX) virgins were collected as black pupa. When eclosed, half of them were provided with males and were allowed to mate overnight, and the other half were kept as virgins. Virgin setting result in all-male progeny whereas mated females produced ~89.5% female progeny under the design used here. Females were provided 15- 20 Sarchophaga bullata hosts in groups of 20 females for 24 hrs to induce production of eggs. The hosts were then removed and females were left overnight (~18 hrs). To collect embryos, individual females were given access to a host at one end (to restrict the oviposition site) and allowed to lay eggs for 6-10 hrs before being removed. Embryos were then harvested immediately (early embryos), 18 hrs later (late embryos), or 51 hrs later (1st instar larvae). All embryos and larvae were collected in an RNase-free environment. The host was cracked open and the "cap" removed to expose embryos. Dissecting needles were used to gently scrape embryos from the surface of the host and transfer them into a 1.5 ml tube pre-chilled on dry ice. Samples were stored at -80º C. If at anytime the host was punctured or embryos were exposed to host hemolymph, they were discarded. Estimates of the number of embryos per replicate (three per life stage/sex) were recorded; early embryos ranged from 300-900, late embryo 140-500, 1st instar larvae 245-520. Since sex cannot be determined at larval stage, some of the mated female hostings were allowed to mature to adulthood then males and females were counted to determine the sex ratio. Early larvae showed an average of 82.9% females and late larvae had an average of 84.2%. Pupae collections were made among the progeny of mated females provided with hosts for 48 hrs. They were sorted by sex and stage (early yellow, red-eye, half black, and black pupae). Equal numbers (S20) of pupae from each stage were then pooled prior to RNA extraction. Males and females were extracted separately. Male reproductive tracts (testes, seminal vesicles, and accessory glands) were dissected in phosphate buffered saline (PBS) from and transferred with a small amount of PBS into a tube on dry ice. A total of 60 testes per replicate were dissected (10 each yellow/red, salt & pepper, and black pupal stages). Female reproductive tracts (30 per replicate) were removed from 1-3 days post eclosion virgin females and transferred to a tube on dry ice.
Growth protocol 18-28 hours post laying; 140-500 individuals per replicate; Male Samples are 100% male, Female Samples are on average 82.9 to 84.2 percent female based on sexing of individuals from matching
Extracted molecule total RNA
Extraction protocol Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
Label Cy5
Label protocol DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.
 
Channel 2
Source name Late female embryos; 18-28 hours post laying; 140-500 individuals per replicate
Organism Nasonia vitripennis
Characteristics Sex: female
developmental stage: late embryos
tissue: whole body
strain: AsymCX
Treatment protocol Samples were prepared at 25º C as follows: Approximately 200 N. vitrirpennis (AsymCX) virgins were collected as black pupa. When eclosed, half of them were provided with males and were allowed to mate overnight, and the other half were kept as virgins. Virgin setting result in all-male progeny whereas mated females produced ~89.5% female progeny under the design used here. Females were provided 15- 20 Sarchophaga bullata hosts in groups of 20 females for 24 hrs to induce production of eggs. The hosts were then removed and females were left overnight (~18 hrs). To collect embryos, individual females were given access to a host at one end (to restrict the oviposition site) and allowed to lay eggs for 6-10 hrs before being removed. Embryos were then harvested immediately (early embryos), 18 hrs later (late embryos), or 51 hrs later (1st instar larvae). All embryos and larvae were collected in an RNase-free environment. The host was cracked open and the "cap" removed to expose embryos. Dissecting needles were used to gently scrape embryos from the surface of the host and transfer them into a 1.5 ml tube pre-chilled on dry ice. Samples were stored at -80º C. If at anytime the host was punctured or embryos were exposed to host hemolymph, they were discarded. Estimates of the number of embryos per replicate (three per life stage/sex) were recorded; early embryos ranged from 300-900, late embryo 140-500, 1st instar larvae 245-520. Since sex cannot be determined at larval stage, some of the mated female hostings were allowed to mature to adulthood then males and females were counted to determine the sex ratio. Early larvae showed an average of 82.9% females and late larvae had an average of 84.2%. Pupae collections were made among the progeny of mated females provided with hosts for 48 hrs. They were sorted by sex and stage (early yellow, red-eye, half black, and black pupae). Equal numbers (S20) of pupae from each stage were then pooled prior to RNA extraction. Males and females were extracted separately. Male reproductive tracts (testes, seminal vesicles, and accessory glands) were dissected in phosphate buffered saline (PBS) from and transferred with a small amount of PBS into a tube on dry ice. A total of 60 testes per replicate were dissected (10 each yellow/red, salt & pepper, and black pupal stages). Female reproductive tracts (30 per replicate) were removed from 1-3 days post eclosion virgin females and transferred to a tube on dry ice.
Growth protocol 18-28 hours post laying; 140-500 individuals per replicate; Male Samples are 100% male, Female Samples are on average 82.9 to 84.2 percent female based on sexing of individuals from matching
Extracted molecule total RNA
Extraction protocol Tissue was homogenized using Trizol reagent (Invitrogen) and extracted RNA was purified using the Qiagen RNeasy protocol with on-column DNase treatment from specific tissues. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).
Label Cy3
Label protocol DNA labeling using 1 O.D. CY-labeled random nonomer primer and 100U Klenow fragment (3>5 exo) per 1 μg double-stranded cDNA in triplicate.
 
 
Hybridization protocol Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybridization master for a given source and biological replicate
Scan protocol Axon GenePix 4200 Professional, 5 micron resolution
Description exp2_matrix_chip1.txt
Data processing Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.
 
Submission date Apr 15, 2013
Last update date Apr 15, 2018
Contact name Justin Choi
E-mail(s) jeochoi@gmail.com
Phone 1-706-721-6757
Organization name Georgia Regents University
Department Cancer Center
Street address 1410 Laney Walker Blvd.
City Augusta
State/province GA
ZIP/Postal code 30912
Country USA
 
Platform ID GPL16800
Series (2)
GSE44701 Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development
GSE46079 Nasonia Tiling Microarray Experiments for Expression Profiling Sexual Development (Embryo18)

Data table header descriptions
ID_REF
VALUE Log2 ratio of Cy5/Cy3, quantile normalized

Data table
ID_REF VALUE
SCAFFOLD1FS000000001 -0.353261762464718
SCAFFOLD1FS000000026 0.4517939697058
SCAFFOLD1FS000000056 -0.47750943246942
SCAFFOLD1FS000000076 -0.510955645547133
SCAFFOLD1FS000000086 -0.296547920841309
SCAFFOLD1FS000000106 0.407427438700205
SCAFFOLD1FS000000131 0.0163750826147844
SCAFFOLD1FS000000161 -0.524721459992383
SCAFFOLD1FS000000171 0.461999282949304
SCAFFOLD1FS000000196 -0.0760912894405372
SCAFFOLD1FS000000226 -0.394248272836919
SCAFFOLD1FS000000236 -0.809365728961524
SCAFFOLD1FS000000266 -0.0216227206794368
SCAFFOLD1FS000000286 -0.163285491838844
SCAFFOLD1FS000000301 -0.109041659492039
SCAFFOLD1FS000000316 -0.330976364583908
SCAFFOLD1FS000000341 -0.242972293675198
SCAFFOLD1FS000000361 0.287493990523203
SCAFFOLD1FS000000386 -0.242473164314225
SCAFFOLD1FS000000406 -0.255963200897606

Total number of rows: 2133888

Table truncated, full table size 82470 Kbytes.




Supplementary file Size Download File type/resource
GSM1123061_277921C01_HX1_U02_Nasonia_532.pair.gz 33.0 Mb (ftp)(http) PAIR
GSM1123061_277921C01_HX1_U02_Nasonia_635.pair.gz 32.7 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data are available on Series record

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