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Sample GSM475998 Query DataSets for GSM475998
Status Public on Nov 26, 2009
Title ATRA treated NB4 cells, 72 hours
Sample type RNA
Source name ATRA treated NB4 cells, 72 hours
Organism Homo sapiens
Characteristics cell line: NB4
treatment: ATRA
time: 72 hours
Treatment protocol NB4 cells were treated with E-6 M ATRA and harvested at 4, 12, 24, 48 and 72 hours, respectively.
Growth protocol NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Protect Midi Kit (Qiagen, Valencia, CA).
Label biotin
Label protocol 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.
Hybridization protocol Fragmented and biotin-labeled cRNA was hybridized to Affymetrix HGU133plus2 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.
Scan protocol Arrays were scanned on an Affymetrix Scanner 3000 7G.
Description gene expression of ATRA treated NB4 cells, 72 hours
Data processing Raw expression data were normalized using Robust Multi-array Averaging (RMA) with quantile normalization.
Submission date Nov 25, 2009
Last update date Aug 28, 2018
Contact name Jiantao Shi
Organization name Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine (RJH-SJTU-SM)
Street address 197 Ruijin Rd II
City Shanghai
State/province Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL570
Series (2)
GSE19201 Expression profiling of ATRA treated NB4 cells
GSE19203 PML-RARa binding sites and their correlation with the gene expression in ATRA treated NB4 cells
Reanalyzed by GSE119087

Data table header descriptions
VALUE RMA-normalized signal intensity.

Data table
1007_s_at 3.809510778
1053_at 7.584578575
117_at 4.576830054
121_at 6.495992662
1255_g_at 1.94220652
1294_at 9.408986689
1316_at 3.560519365
1320_at 2.838225312
1405_i_at 8.575368443
1431_at 3.366794176
1438_at 3.413945105
1487_at 8.500995508
1494_f_at 4.546747602
1552256_a_at 7.743383374
1552257_a_at 7.261168874
1552258_at 3.483599987
1552261_at 2.658227674
1552263_at 4.24466774
1552264_a_at 6.186084282
1552266_at 2.247691603

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM475998_NB4_ATRA_72H.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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