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Sample GSM475996 Query DataSets for GSM475996
Status Public on Nov 26, 2009
Title ATRA treated NB4 cells, 24 hours
Sample type RNA
 
Source name ATRA treated NB4 cells, 24 hours
Organism Homo sapiens
Characteristics cell line: NB4
treatment: ATRA
time: 24 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, 24 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
E-mail(s) jtshi@sibs.ac.cn
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
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE RMA-normalized signal intensity.

Data table
ID_REF VALUE
1007_s_at 3.900205275
1053_at 8.287437249
117_at 3.577459771
121_at 6.522954146
1255_g_at 2.146606453
1294_at 5.829164913
1316_at 3.953940049
1320_at 2.999110636
1405_i_at 9.659293236
1431_at 2.761462072
1438_at 3.403984046
1487_at 8.40755563
1494_f_at 4.914280915
1552256_a_at 9.011219018
1552257_a_at 8.673491822
1552258_at 3.905159633
1552261_at 2.823917411
1552263_at 4.12923833
1552264_a_at 6.028707511
1552266_at 2.065116861

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM475996_NB4_ATRA_24H.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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