NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM225318 Query DataSets for GSM225318
Status Public on Aug 30, 2007
Title IU/Hahn_Drosophila_134B
Sample type RNA
 
Source name D. melanogaster embryo 5 hours
Organism Drosophila melanogaster
Characteristics 30-50 embryos from line 134
Extracted molecule total RNA
Extraction protocol Two RNA samples per line per time point (5 and 8 hours) were extracted using manufacturer's TRIzol reagent protocol (Invitrogen, Carlsbad, CA). The concentrations of these samples were tested using a spectrophotometer and Na2HPO4 spec solution. The 36 samples (9 lines x 2 time points x 2 samples) of extracted RNA were labeled using the one-cycle cDNA Synthesis protocol from Affymetrix. cDNA was made from the extracted RNA by first making a T7-Oligo(dT) Primer Master Mix and letting it incubate with the samples for 10 min at 700C and cooling for 2min at 40C. A First-Strand Master Mix was added and the samples were incubated for 2 min at 420C. After 200U/μL SuperScript II was added the samples were incubated for an additional hour at 420C and then cooled at 40C for 2min. A Second-Strand Master Mix was added to the samples and then they were incubated at 160C for 2 hours and then cooled for 2min at 40C. The samples were incubated for another
5min at 160C after T4 DNA Polymerase was added, the samples were cooled at 40C for 2min and 0.5M EDTA was added. The now double stranded cDNA was cleaned up using spin columns and 100% Ethanol.
Label biotin
Label protocol An IVT Reaction mix was added to the samples to synthesis Biotin-Labeled cRNA, and they were allowed to incubate at 370C overnight (~16 hours). The newly Biotin-labeled cRNA was cleaned up and quantified using a spectrophotometer. Sample purity was between 1.96 and 1.7 (A260/A280). Fragmented samples were then stored at –200C until hybridizations.
 
Hybridization protocol Hybridizations to the Affymetrix Drosophila 2.0 GeneChip microarray took place in the Microarray Core Facility at UC Davis.
Scan protocol Hybridizations to the Affymetrix Drosophila 2.0 GeneChip microarray took place in the Microarray Core Facility at UC Davis.
Description Sample 2 from this line
Data processing Standard Affymetrix data processing
 
Submission date Aug 28, 2007
Last update date Aug 28, 2018
Contact name Matthew W. Hahn
E-mail(s) [email protected]
Organization name Indiana University
Department Department of Biology
Street address 1001 E. 3rd St.
City Bloomington
State/province IN
ZIP/Postal code 47405
Country USA
 
Platform ID GPL1322
Series (1)
GSE8892 Abundant genetic variation in transcript level during early Drosophila development
Relations
Reanalyzed by GSE119084

Data table header descriptions
ID_REF
VALUE Expression level
ABS_CALL Gene expression present or absent
DETECTION P-VALUE P-value threshold

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 436.547 P 4.42873e-05
AFFX-BioB-M_at 808.534 P 4.42873e-05
AFFX-BioB-3_at 604.931 P 4.42873e-05
AFFX-BioC-5_at 1323.91 P 4.42873e-05
AFFX-BioC-3_at 871.495 P 4.42873e-05
AFFX-BioDn-5_at 2412.23 P 4.42873e-05
AFFX-BioDn-3_at 4098.42 P 4.42873e-05
AFFX-CreX-5_at 8268.86 P 5.16732e-05
AFFX-CreX-3_at 8455.61 P 4.42873e-05
AFFX-DapX-5_at 692.601 P 4.42873e-05
AFFX-DapX-M_at 986.552 P 4.42873e-05
AFFX-DapX-3_at 1778.29 P 4.42873e-05
AFFX-LysX-5_at 67.3609 P 4.42873e-05
AFFX-LysX-M_at 120.676 P 4.42873e-05
AFFX-LysX-3_at 293.563 P 4.42873e-05
AFFX-PheX-5_at 112.439 P 4.42873e-05
AFFX-PheX-M_at 195.546 P 4.42873e-05
AFFX-PheX-3_at 289.438 P 4.42873e-05
AFFX-ThrX-5_at 144.059 P 5.16732e-05
AFFX-ThrX-M_at 288.025 P 4.42873e-05

Total number of rows: 18952

Table truncated, full table size 578 Kbytes.




Supplementary file Size Download File type/resource
GSM225318.CEL.gz 1.3 Mb (ftp)(http) CEL
GSM225318.CHP.gz 123.2 Kb (ftp)(http) CHP
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap