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Sample GSM1668922 Query DataSets for GSM1668922
Status Public on Apr 29, 2015
Title MDS-L_NCD38_48h_rep3
Sample type RNA
 
Source name MDS-L, NCD38, 48h, replicate3
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 NCD38
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
E-mail(s) machakm6@kuhp.kyoto-u.ac.jp
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
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_23_P117082 -0.32170296
A_33_P3246448 0.280941
A_33_P3318220 -0.06734061
A_33_P3236322 -0.28304172
A_33_P3319925 -0.042333603
A_21_P0000509 -0.60014725
A_21_P0000744 0.4659853
A_24_P215804 0.20903683
A_23_P110167 -0.12230587
A_33_P3211513 -0.669343
A_23_P103349 0.1690762
A_32_P61480 -0.1277237
A_33_P3788124 0.01710105
A_33_P3414202 0.18285847
A_33_P3316686 0.13463879
A_33_P3300975 0.19943881
A_33_P3263061 -0.22104359
A_33_P3261373 0.020638227
A_24_P278460 -0.068323135
A_21_P0013109 0.33599377

Total number of rows: 50737

Table truncated, full table size 1243 Kbytes.




Supplementary file Size Download File type/resource
GSM1668922_US45102837_253949419105_S01_GE1_1100_Jul11_2_4.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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