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Sample GSM1668917 Query DataSets for GSM1668917
Status Public on Apr 29, 2015
Title MDS-L_DMSO_48h_rep1
Sample type RNA
Source name MDS-L, DMSO, 48h, replicate1
Organism Homo sapiens
Characteristics cell line: MDS-L
cell type: leukemia
Treatment protocol NCD38 or NCD25 was dissolved in Dimethyl Sulfoxide (DMSO). 5-7x10^5 Cells were seeded in 6 well plates. 2 micromolar NCD38, NCD25 or DMSO was added and incubated for 48 hours at 37 ºC in the incubator with 5% CO2.
Growth protocol HEL and CMK11-5 were cultured in 10% heat-inactivated fetal bovine serum (FBS) containing RPMI medium. MDS-L was cultured in the same medium with 20ng/ml human IL-3 (PEPRO TECH) and 20M 2-mercaptoethanol (Gibco)
Extracted molecule total RNA
Extraction protocol RNA was extracted using RNA easy mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using the NanoDrop-1000 spectrophotometer. Quality of total RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol 150ng total RNA was labeled with Cyanine-3 (Cy3) using Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer’s protocol, followed by RNAeasy column purification (QIAGEN). Dye incorporation was checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600ng Cy3-Labeled cRNA was fragmented using Gene Expression Hybridization Kit (Agilent) according to the manufacturer’s protocol and hybridized to SurePrint G3 Human GE Microarray 8 x 60K Ver2.0 (G4858A) (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with GE Wash Buffer 1 and Buffer 2 (Agilent).
Scan protocol Microarray slides were scanned immediately after washing on the Microarray Scanner G2565BA (Agilent) 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 Gene expression of MDS-L after 48hr incubation with DMSO
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Apr 28, 2015
Last update date Apr 29, 2015
Contact name Masahiro Kawahara
Phone +81757514964
Organization name Kyoto University
Department Hematology Oncology
Lab leukemia research
Street address 54 Shogoin-Kawahara-cho, Sakyo-ku,
City Kyoto
State/province State...
ZIP/Postal code 6068507
Country Japan
Platform ID GPL17077
Series (1)
GSE68348 Differential gene expression profiling by LSD1 inhibition using novel LSD1 inhibitors (NCD25 and NCD38)

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P117082 0.072050095
A_33_P3246448 -0.05026388
A_33_P3318220 0.007911682
A_33_P3236322 -1.790961
A_33_P3319925 -0.48137665
A_21_P0000509 0.6570759
A_21_P0000744 -0.16517162
A_24_P215804 0.006960869
A_23_P110167 0.27686214
A_33_P3211513 0.057541847
A_23_P103349 0.05679965
A_32_P61480 0.16487479
A_33_P3788124 -0.017100811
A_33_P3414202 -0.07544613
A_33_P3316686 0.030090332
A_33_P3300975 -0.6480589
A_33_P3263061 0.059963226
A_33_P3261373 -0.4082446
A_24_P278460 -0.043787956
A_21_P0013109 0.07816267

Total number of rows: 50737

Table truncated, full table size 1241 Kbytes.

Supplementary file Size Download File type/resource
GSM1668917_US45102837_253949416596_S01_GE1_1100_Jul11_1_3.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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