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Sample GSM787997 Query DataSets for GSM787997
Status Public on Sep 13, 2011
Title 4796
Sample type genomic
 
Source name fly body
Organism Drosophila simulans
Characteristics genotype: XX
nucleic acid: DNA
autosome: c167.4
x origin: c167.4
Sex: F
rep: 2
Extracted molecule genomic DNA
Extraction protocol Flies were freeze dried at -20° overnight prior to homogenization. Dried flies were ground to a fine powder using a GenoGrinder (Maximum, three minutes, repeated twice). Trizol (1 ml) was added to each homogenized sample and mixed thoroughly in the GenoGrinder (Max, 3 minutes). Samples were transferred to a new tube, 1 ul linear acrylamide was added to each and samples were then incubated at room temperature for 5 minutes. RNA was extracted using a standard Trizol extraction protocol: phase separation using 0.1 vol BCP, RNA precipitation with isopropanol, 70% ethanol wash and resuspension in 80 ul DEPC H2O. Concentration was measured using a NanoDrop and up to 30 ug RNA per sample was treated with DNase I in 100 ul reaction volumes for 30 minutes at 37° (reaction mix: 4U Cloned DNase I TaKaRa 2220A, 80U Promega Recombinant RNasin N2515, in 1X TaKaRa Cloned DNase I Buffer II). Samples were cleaned prior to concentration using the Qiagen RNeasy Mini Kit (Cat. # 74104) following the manufacturer’s standard protocol with 30 ul DEPC H2O elutions (run through the column twice). RNA quality was examined using BioAnalyzer RNA 6000 Nano chips and all samples were found to be of good quality. Genomic DNA was isolated from 35-40 flash frozen females using the AllPrep Mini Kit (Qiagen) following standard manufacturer’s protocols. Samples were concentrated by standard ethanol precipitation and resuspended in 31 ul DEPC H2O.
Label biotin
Label protocol For each sample, target material was prepared for array hybridization using recommended Affymetrix® kits following the GeneChip© WT Double-Stranded Target Assay Manual protocol for single Tiling Arrays (no amplification) Ch3 . Procedures A-D. Briefly, 10 ug of Total RNA was concentrated to 8ul in DEPC H2O and 1st and 2nd strand cDNA were synthesized using the WT Double-Stranded DNA Synthesis Kit (P/N 900813). Following Cleanup (P/N 900371), 7.5 ug of dsDNA was fragmented and labeled following the standard protocol (WT Double-Stranded DNA Terminal Labeling Kit, P/N 900812).
 
Hybridization protocol The prepared target samples were then hybridized using the Hybridization, Wash and Stain Kit (P/N 900720) following the manufacturer’s protocol for the Fluidics Station 450 with protocol FS450_0001.
Scan protocol Arrays were scanned using an Affymetrix® 7G scanner.
Description 4796 CR-2_(dros_snpa520726F).CEL
Data processing Signals were extracted from the scans using the apt-cel-extract program of the Affymetrix Powel Tools® (version 1.10.2) suite. GC bin control probes provide an estimate of non-specific hybridization (Affymetrix 2005) and help to assess the overall quality of the hybridization. A GC bin control is a standard Affymetrix® control based upon the number of G/C bases (from 3 to 24) in the 25 mer probe. None of the GC bin control probes align to the D. melanogaster or D. simulans reference genomes. Individual probes were classified according to their GC content and matched to the corresponding GC bin controls. A probe was considered detected when signal strength was higher than the median intensity of the corresponding GC band controls. Detection above background (DABG) was calculated at the individual probe level.
To correct for the background noise and to normalize the probe signals, each probe was classified into a GC bin and the 5 percentile signal for that GC bin was subtracted from the probe. The expression of a probe set was estimated by the natural log of the arithmetic mean of individual probe signals.
 
Submission date Aug 30, 2011
Last update date Sep 14, 2011
Contact name Yajie Yang
E-mail(s) yyj920@gmail.com
Organization name UF
Street address 2033 Mowry Road Room 118
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL11273
Series (1)
GSE31750 Verification of a custom chip which measures abundance, isoforms and alleles in Drosophila

Data table header descriptions
ID_REF
VALUE Background-corrected, normalized, log-transformed signal

Data table
ID_REF VALUE
ase-136992_16 1.0986122887
ase-136992_22 2.302585093
ase-136992_23 1.9459101491
ase-193163_16 2.302585093
ase-193163_17 2.0794415417
ase-193163_22 2.7725887222
ase-193163_23 1.3862943611
ase-431968_0 1.3862943611
ase-431968_1 1.6094379124
ase-431968_6 2.0794415417
ase-431968_7 1.3862943611
ase-454029_0 -73.68272298
ase-454029_1 1.0986122887
ase-454029_6 2.0794415417
ase-454029_7 2.8903717579
ase-52757_8 2.0794415417
ase-52757_15 2.302585093
ase-52757_16 1.0986122887
ase-52757_17 0.6931471806
ase-52757_22 2.6390573296

Total number of rows: 2461622

Table truncated, full table size 61637 Kbytes.




Supplementary file Size Download File type/resource
GSM787997_4796_CR-2_dros_snpa520726F_.CEL.gz 7.4 Mb (ftp)(http) CEL
GSM787997_4796_annotated_dump.csv.gz 25.4 Mb (ftp)(http) CSV
Processed data included within Sample table
Processed data provided as supplementary file

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