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Sample GSM539384 Query DataSets for GSM539384
Status Public on May 05, 2010
Title embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 2 dye swap
Sample type RNA
 
Channel 1
Source name EIn(1)103.8_2
Organism Drosophila melanogaster
Characteristics developmental stage: embryo
age: 0-21hour
tissue: whole embryos
strain: inversion EIn(1)103.8
Biomaterial provider Original stocks from DrosDel http://www.drosdel.org.uk/
Treatment protocol Embryos laid over a 21hr period at 25C were dechorionated in bleach and transfered to Trizol, approximately 1000 embryos per aliquot
Growth protocol Flies maintained at 25 degrees C on standard cornmeal agar then transferred to cages on standard apple juice agar plates with yeast paste at 25C for egg collection
Extracted molecule total RNA
Extraction protocol Medium scale RNA extraction using TRIzol (http://www.flychip.org.uk/protocols/gene_expression/)
Label Cy3
Label protocol Direct Labelling: Up to 50µg total RNA are mixed with anchored oligo (dT)23 (Sigma). The RNA is reverse transcribed using Superscript III (Invitrogen). Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated during cDNA synthesis. (http://www.flychip.org.uk/protocols/gene_expression)
 
Channel 2
Source name cis103.8_2
Organism Drosophila melanogaster
Characteristics developmental stage: embryo
age: 0-21hour
tissue: whole embryos
strain: progenitor cis103.8
Biomaterial provider Original stocks from DrosDel http://www.drosdel.org.uk/
Treatment protocol Embryos laid over a 21hr period at 25C were dechorionated in bleach and transfered to Trizol, approximately 1000 embryos per aliquot
Growth protocol Flies maintained at 25 degrees C on standard cornmeal agar then transferred to cages on standard apple juice agar plates with yeast paste at 25C for egg collection
Extracted molecule total RNA
Extraction protocol Medium scale RNA extraction using TRIzol (http://www.flychip.org.uk/protocols/gene_expression/)
Label Cy5
Label protocol Direct Labelling: Up to 50µg total RNA are mixed with anchored oligo (dT)23 (Sigma). The RNA is reverse transcribed using Superscript III (Invitrogen). Cy3-dCTP or Cy5-dCTP (GE Healthcare) are incorporated during cDNA synthesis. (http://www.flychip.org.uk/protocols/gene_expression)
 
 
Hybridization protocol Hybridisation to amino-modified long oligonucleotide microarrays using a Genomic Solutions hybridisation station with the Biosolutions hybridisation buffer (http://www.flychip.org.uk/protocols/hybridisation/)
Scan protocol Operating instructions for the Genepix 4000B dual laser scanner (http://www.flychip.org.uk/protocols/imaging/)
Description embryo inversion EIn(1)103.8 vs progenitor cis103.8 replicate 2 dye swap
Data processing Spot finding and quantitation via the Dapple package. VSN-normalised experiment/control ratio equivalent to log[2] ratio.
 
Submission date Apr 30, 2010
Last update date May 04, 2010
Contact name Lisa Meadows
E-mail(s) l.meadows@gen.cam.ac.uk
Organization name University of Cambridge
Department Department of Genetics
Lab FlyChip
Street address Downing Street
City Cambridge
ZIP/Postal code CB2 3EH
Country United Kingdom
 
Platform ID GPL8244
Series (1)
GSE21607 Expression differences between inversions and their progenitors in Drosophila melanogaster embryos

Data table header descriptions
ID_REF
VALUE VSN normalised experiment/control ratio equivalent to log[2] ratio
A VSN normalised average intensity
Status1_col Spotfinding status channel 1; A = [A]ccepted, R =[R]ejected, S=[S]uspicious
fgMedian1_col foreground (spot) median pixel intensity of channel 1
bgMedian1_col background (local area around spot) median pixel intensity of channel 1
fgAdjMAD1_col foreground (spot) pixel intensity variability of channel 1
bgAdjMAD1_col background (local area around spot) pixel intensity variability of channel 1
Status2_col Spotfinding status channel 2; A = [A]ccepted, R =[R]ejected, S=[S]uspicious
fgMedian2_col foreground (spot) median pixel intensity of channel 2
bgMedian2_col background (local area around spot) median pixel intensity of channel 2
fgAdjMAD2_col foreground (spot) pixel intensity variability of channel 2
bgAdjMAD2_col background (local area around spot) pixel intensity variability of channel 2
fgN_col number of pixels in the foreground
bgN_col number of pixels in the background

Data table
ID_REF VALUE A Status1_col fgMedian1_col bgMedian1_col fgAdjMAD1_col bgAdjMAD1_col Status2_col fgMedian2_col bgMedian2_col fgAdjMAD2_col bgAdjMAD2_col fgN_col bgN_col
ID100003970200000100 -0.262633858435613 16.5046896595922 R 90 80 31.1346 22.239 R 61 50 29.652 23.7216 225 1023
ID100003438000000200 -0.219399647266737 17.3256167594184 A 136 79 59.304 25.2042 A 94 50 45.9606 22.239 293 935
ID100004362000000300 -0.344745890525154 19.2501707105189 A 410 75 115.643 23.7216 A 324 49 111.195 20.7564 349 851
ID100004016400000500 -0.537342211996908 20.8368135955293 A 1094 77 302.45 23.7216 A 1004 49 286.142 20.7564 349 851
ID100004239600000600 -0.782109635025481 18.1639543948866 A 185 83 69.6822 26.6868 A 185 54 81.543 23.7216 293 935
ID100004090200000700 -0.192847535621041 23.1804381083113 A 6106 83 2788.77 26.6868 A 4465 54 2093.43 26.6868 349 851
ID100003631800000800 -0.266644578143175 19.1566711298483 A 396 78 123.056 22.239 A 297 50 118.608 20.7564 293 935
ID100003360600000900 0.0753482019083709 16.0322612518003 R 79 75 26.6868 23.7216 R 45 48 17.7912 22.239 225 1023
ID100003207600001200 -0.581369341339872 17.5476318965522 A 139 77 50.4084 20.7564 A 119 49 56.3388 20.7564 293 935
ID100004400400001300 -0.436688132295796 18.3704973556947 A 231 81 66.717 23.7216 A 189 50 65.2344 22.239 225 1023
ID100004356600001400 0.283688761056219 16.2804443926547 R 92 82 25.2042 23.7216 R 48 51 20.7564 22.239 225 1023
ID100004131000001500 -0.441646731497226 20.1157698962305 A 698 80 179.395 23.7216 A 596 49 174.947 20.7564 225 1023
ID100003322200001600 -0.270588071727559 18.1265494907695 A 210 80 60.7866 23.7216 A 154 51 69.6822 22.239 293 935
ID100003471000001700 0.103960498515853 17.2448625607518 A 142 78 53.3736 22.239 A 82 51 40.0302 20.7564 177 1111
ID100004129200001800 -0.0298809325065044 17.6597284151699 A 172 75 59.304 20.7564 A 108 51 53.3736 20.7564 293 935
ID100004323000000001 -0.0412871185879844 16.3689219179954 R 89 79 23.7216 23.7216 R 54 48 26.6868 22.239 225 1023
ID100003934800000101 0.0265715939421796 16.8597145086927 S 114 86 45.9606 26.6868 R 68 52 34.0998 26.6868 349 851
ID100003279600000201 -0.331888283716701 17.1732576901171 S 122 83 48.9258 26.6868 S 89 49 47.4432 23.7216 349 851
ID100003202200000301 -0.609909180462434 19.5552228925447 A 458 76 295.037 20.7564 A 433 49 272.798 20.7564 349 851
ID100003894000000401 -0.295702249875109 17.3775748867137 A 137 74 65.2344 22.239 A 99 48 48.9258 22.239 293 935

Total number of rows: 14569

Table truncated, full table size 1622 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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