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Sample GSM475994 Query DataSets for GSM475994
Status Public on Nov 26, 2009
Title ATRA treated NB4 cells, 4 hours
Sample type RNA
Source name ATRA treated NB4 cells, 4 hours
Organism Homo sapiens
Characteristics cell line: NB4
treatment: ATRA
time: 4 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, 4 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 3.717999412
1053_at 8.835977664
117_at 3.291560288
121_at 6.554928142
1255_g_at 2.33688139
1294_at 4.871235742
1316_at 4.04997945
1320_at 2.922844776
1405_i_at 9.571125469
1431_at 2.969967575
1438_at 3.316467106
1487_at 8.645654716
1494_f_at 4.730223469
1552256_a_at 9.529318992
1552257_a_at 8.794257031
1552258_at 3.04828603
1552261_at 2.923283978
1552263_at 3.814580382
1552264_a_at 6.014960676
1552266_at 2.175600842

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM475994_NB4_ATRA_4H.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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