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Sample GSM1000731 Query DataSets for GSM1000731
Status Public on Apr 23, 2013
Title 6h_DMSO_rep2
Sample type RNA
 
Channel 1
Source name HD-MEL cells
Organism Mus musculus
Characteristics cell type: High differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.
treatment: DMSO
time: 6h
cell line: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)
Treatment protocol MEL cells were washed in PBS, and stored at -80 °C.
Growth protocol MEL cells were cultured in RPMI1640 medium with 10% fetal calf serum at 37 °C with 5% CO2 concentration.
Extracted molecule total RNA
Extraction protocol Total RNA of MEL cells was extracted using RNeasy Mini Kit (Qiagen).
Label Cy3
Label protocol Twenty mg of the total RNA was labeled with amino-modified dNTP using a SuperScript Indirect cDNA Labeling System (Invitrogen). The amino-modified cDNA was purified with a S.N.A.P column (Invitrogen) and ethanol precipitation. The purified cDNA was labeled with Cye3 Mono-Reactive Dye Pack (Amersham Biosciences) or Cye5 Mono-Reactive Dye Pack (Amersham Biosciences) by coupling reaction. The labeled cDNA was purified with a QIAquick PCR Purification Kit (Qiagen).
 
Channel 2
Source name LD-MEL cells
Organism Mus musculus
Characteristics treatment: DMSO
time: 6h
cell type: Low differentiation-inducible murine erythroleukemia cells, A clone of T-3-Cl-2-0.fl.
cell line: T-3-Cl-2-0.fl (Riken Cell No. RCB0561)
Treatment protocol MEL cells were washed in PBS, and stored at -80 °C.
Growth protocol MEL cells were cultured in RPMI1640 medium with 10% fetal calf serum at 37 °C with 5% CO2 concentration.
Extracted molecule total RNA
Extraction protocol Total RNA of MEL cells was extracted using RNeasy Mini Kit (Qiagen).
Label Cy5
Label protocol Twenty mg of the total RNA was labeled with amino-modified dNTP using a SuperScript Indirect cDNA Labeling System (Invitrogen). The amino-modified cDNA was purified with a S.N.A.P column (Invitrogen) and ethanol precipitation. The purified cDNA was labeled with Cye3 Mono-Reactive Dye Pack (Amersham Biosciences) or Cye5 Mono-Reactive Dye Pack (Amersham Biosciences) by coupling reaction. The labeled cDNA was purified with a QIAquick PCR Purification Kit (Qiagen).
 
 
Hybridization protocol Microarray was pre-hybrized at 50°C, 60 minutes in 5 x saline sodium citrate buffer (SSC) contained 0.1% sodium dodecyl sulfate (SDS)and 0.1% bovine serum albumin (BSA), washed with water, and rinsed with isopropanol. Mixed Cy3 and Cy5 labeled cDNA solution was denaturation at 95°C, 5 minutes in 5 x SSC contained 1.67 mg/mL acetylated BSA. After cooling, SDS was added to final concentration 0.33%. The microarray was covered with a Gap cover glass (Matsunami), hybridization solution was injected, and the microarray was placed in a hybridization cassette (TeleChem). Hybridization was performed at 50°C for 14 hours. After hybridization, the microarray was washed using a Wash Station (TeleCham) as follow; at 42°C 5 minutes in 2 x SSC contained 0.1%SDS, at room temperature 10 minutes in 0.1 x SSC contained 0.1%SDS, and finally twice in 0.1 x SSC at room temperature for 2min. The microarray was dried by centrifugation.
Scan protocol Hybridization images were scanned using a ScanArray 5000(Perkin-Elmer). Fluorescence intensity of the microarray was quantified using QuantArray 3.0 software (Perkin-Elmer).
Description Technical replicate 2 of 4. 6 hours after 1.0% DMSO treatment.
target HD-MEL
control LD-MEL
Data processing The microarray data was analyzed using GeneSpring 6.0 (Silicon Genetics). Intensity difference between Cy3 and Cy5 was normalized by LOWESS method.
Signal intensities were higher than negative spot.
 
Submission date Sep 10, 2012
Last update date Apr 24, 2013
Contact name Hitoshi Sasaki
E-mail(s) [email protected]
Organization name Tokyo University of Science
Department Department of Biological Science and Technology
Lab Murakami Laboratory
Street address 2641 Yamazaki
City Noda
State/province Chiba
ZIP/Postal code 278-8510
Country Japan
 
Platform ID GPL16035
Series (1)
GSE40754 Comparison of transcriptome of high differentiation-inducible murine erythroleukemia cells and low differentiation-inducible murine erythroleukemia cells

Data table header descriptions
ID_REF
VALUE Log2 Lowess HD MEL/LD MEL
PRE_VALUE Lowess HD MEL/LD MEL

Data table
ID_REF VALUE PRE_VALUE
H3001A01 0.7094 1.6351149
H3001A02 -0.0921 0.9381844
H3001A03 0.0834 1.0595181
H3001A04 0.1592 1.1166759
H3001A05
H3001A06 0.3868 1.3074722
H3001A07 -0.2845 0.8210242
H3001A08 0.5575 1.4717119
H3001A09 0.0970 1.0695431
H3001A10 -0.0117 0.9918963
H3001A11 -0.1645 0.8922299
H3001A12 -0.1942 0.87408715
H3001B01 1.3136 2.4855678
H3001B02 0.0787 1.0560353
H3001B03 0.0233 1.0163114
H3001B04 0.1279 1.0926746
H3001B05 0.2962 1.2279404
H3001B06 0.0881 1.0629495
H3001B07 0.3879 1.3085068
H3001B08 -0.1554 0.89789754

Total number of rows: 22656

Table truncated, full table size 555 Kbytes.




Supplementary file Size Download File type/resource
GSM1000731_DMSO_06h-2-part1.txt.gz 113.8 Kb (ftp)(http) TXT
GSM1000731_DMSO_06h-2_part2.txt.gz 98.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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