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Sample GSM1020784 Query DataSets for GSM1020784
Status Public on Jan 30, 2023
Title Hdac1 vs WT replicate 3
Sample type RNA
 
Channel 1
Source name Oregon-R Wild type
Organism Drosophila melanogaster
Characteristics background strain: Oregon-R
genotype/variation: Wild type
Stage: 3rd instar larvae
Growth protocol Fly grew at 25 degree C, harvest at 3rd instar stage
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
After DNaseI treatment, RNA were purified by RNeasy kit (Qiagene)
Label Alexa Fluor 555
Label protocol 15 µg of total RNA were primed with 2 µl of 2.5 µg/µl anchored Oligo-(dT)20 primer at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen). After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min. to degrade RNA. Neutralize the hydrolysis reaction by adding 25μL 1M HEPES pH 7.4. After clean by QIAquick(Qaigen), cDNA were elute from column by 60 μl 0.1M NaHCO3 pH 9.0. Add elute into a tube contain Alexa 555 or 647 NHS ester. Couple the dye at room temperature in the dark for 60-90 min. Stop the reaction by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Immediately purify the labeled cDNA through QIAquick column.
 
Channel 2
Source name Oregon-R Hdac1 mutant
Organism Drosophila melanogaster
Characteristics background strain: Oregon-R
genotype/variation: Hdac1[303]/Hdac1[def8]
Stage: 3rd instar larvae
Growth protocol Fly grew at 25 degree C, harvest at 3rd instar stage
Extracted molecule total RNA
Extraction protocol Total RNA extracted using Trizol following manufacturer's instructions
After DNaseI treatment, RNA were purified by RNeasy kit (Qiagene)
Label Alexa Fluor 647
Label protocol 15 µg of total RNA were primed with 2 µl of 2.5 µg/µl anchored Oligo-(dT)20 primer at 70°C for 10 min, then reversed transcribed at 46°C for 2 h in the presence of 400 U SuperScript III RTase, and 10mM dNTP including amino-allyl-dUTP. (SuperScript Indirect cDNA Labeling System, Invitrogen). After reaction, add 10μL 0.5M EDTA and 10μL 1N NaOH, incubate at 70℃ for 15 min. to degrade RNA. Neutralize the hydrolysis reaction by adding 25μL 1M HEPES pH 7.4. After clean by QIAquick(Qaigen), cDNA were elute from column by 60 μl 0.1M NaHCO3 pH 9.0. Add elute into a tube contain Alexa 555 or 647 NHS ester. Couple the dye at room temperature in the dark for 60-90 min. Stop the reaction by adding 15 μl of 4 M NH2OH-HCl in the dark for 15 min. Immediately purify the labeled cDNA through QIAquick column.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent Hi-RPM Gene Expression Hybridization Kit,) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Gene Expression Wash Buffer Kit and dry.
Scan protocol Scanned on an Agilent G2565CA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.10.5.1.1).
Description Biological replicate 3 of 4. WT or Hdac1 mutant were harvest at 3rd instar stage
Data processing Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.
 
Submission date Oct 17, 2012
Last update date Jan 30, 2023
Contact name Der-Hwa Huang
E-mail(s) mbdhuang@ccvax.sinica.edu.tw
Organization name Academia Sinica
Department Insititute of Molecular Biology
Lab N420
Street address 128, Sec2, Academia Rd.
City Nankang, Taipei
State/province Taiwan
ZIP/Postal code 11529
Country Taiwan
 
Platform ID GPL16193
Series (1)
GSE41640 Oregon-R: Control vs. Hdac1 mutant

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Alexa Fluor 647/Alexa Fluor 555) representing test/reference

Data table
ID_REF VALUE
1 1.740752509e-002
2 0.000000000e+000
3 0.000000000e+000
4 0.000000000e+000
5 0.000000000e+000
6 0.000000000e+000
7 0.000000000e+000
8 0.000000000e+000
9 0.000000000e+000
10 0.000000000e+000
11 0.000000000e+000
12 0.000000000e+000
13 1.560527115e-001
14 6.561270533e-002
15 2.651895856e-001
16 2.555902849e-001
17 -1.111317902e-001
18 -4.396602594e-002
19 0.000000000e+000
20 -5.071210817e-002

Total number of rows: 45109

Table truncated, full table size 1021 Kbytes.




Supplementary file Size Download File type/resource
GSM1020784_Hdac1_OR_3.txt.gz 4.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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