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Sample GSM1060441 Query DataSets for GSM1060441
Status Public on Aug 27, 2013
Title 3h_USP2KD_treated_2
Sample type RNA
 
Source name differentated 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells for 3 hrs
Organism Mus musculus
Characteristics cell line: 3T3-L1
cell type: adipocytes
Treatment protocol After differentiation, 3T3-L1 cells were treated with 2-fold diluted supernatant with supernatants of USP2 knockdown or mock transfected HL-60 cells for 3 or 6 hrs. Supernatants were prepared from 5 day culture of USP2 knockdown or control cells in Opti medium (Invitrogen) with 30nM PMA
Growth protocol 3T3-L1 cells were grown in DMEM with 10% FCS. For differentiation into adipocyte-like cells, we cultured the cells in the adipogenic medium (Takara) for 1 week.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was prepared with TRIzol reagent according to a manual.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp WT Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description 3T3-L1 cells stimulated with supernatant of USP2 knockdown HL-60 cells, 3h, biological rep 2
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid:028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized signal intensity calculated using GeneSpring 12.1GX. Setting is : Advanced Flag Import (Feature is not positive and significant, Not Detected; Feature in not Uniform, Compromised; Feature is not above background, Not Detected; Feature is Saturated, Compromised; Feature is a population outlier, Compromised), Normalization Option (Threshold raw signals to 1.0; Normaliation algorithm, Percentile Shift; Percentile target, 75), Preprocess Baseline Options (Do not perform baseline transformation)
 
Submission date Jan 07, 2013
Last update date Aug 27, 2013
Contact name Hiroshi Kitamura
E-mail(s) ktmr@rakuno.ac.jp
Phone 81-11-388-4781
Organization name Rakuno Gakuen University
Department School of Veterinary Medicine
Lab Laboratory for Veterinary Physiology
Street address 582 Midorimachi, Bunkyodai
City Ebetsu
ZIP/Postal code 069-8501
Country Japan
 
Platform ID GPL10787
Series (1)
GSE43313 Effects of supernatants of USP2 knockdown HL-60 cells and mock transfected HL60 cells on differentiated 3T3-L1 cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
(+)E1A_r60_1 9.290744
(+)E1A_r60_3 -7.1170263
(+)E1A_r60_a104 -6.9088283
(+)E1A_r60_a107 -2.89604
(+)E1A_r60_a135 0.2142191
(+)E1A_r60_a20 1.2631207
(+)E1A_r60_a22 3.1077747
(+)E1A_r60_a97 5.388088
(+)E1A_r60_n11 7.3119917
(+)E1A_r60_n9 8.04609
3xSLv1 -7.226748
A_30_P01017425 -2.4229894
A_30_P01017426 -2.949314
A_30_P01017427 -5.070712
A_30_P01017428 -1.965611
A_30_P01017429 -7.1790504
A_30_P01017430 -4.586774
A_30_P01017431 -7.1587934
A_30_P01017432 -3.1316457
A_30_P01017433 -3.4241586

Total number of rows: 55821

Table truncated, full table size 1332 Kbytes.




Supplementary file Size Download File type/resource
GSM1060441_SG11484150_252800514542_S001_GE1_107_Sep09_1_4.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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