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Sample GSM1032115 Query DataSets for GSM1032115
Status Public on Feb 16, 2013
Title TC-5 µM treament
Sample type RNA
 
Source name human day 8 differentiated erythroid cells
Organism Homo sapiens
Characteristics drug treatment: TC-5 µM
Treatment protocol Tranylcypromine (Tocris Bioscience) dissolved in water at 0.5, 1.5 and 5 µM was added to the culture medium on day 4 through day 14.
Growth protocol From days 0 to 8, the cells were cultured in IMDM basic medium (Biochrom) supplemented with 40 µg of inositol/ml, 10 µg of folic acid/ml, 160 µM monothioglycerol, 120 µg of iron-saturated human transferrin/ ml, 10 µg of insulin/ml, 900 ng of ferrous sulfate/ml, 90 ng of ferric nitrate/ml, 1µM hydrocortisone, and 5 ng of interleukin-3 (IL-3)/ml, and 200 mM L-glutamine (Invitrogen), 1% deion- ized bovine serum albumin (Stemcell Technologies), 100 ng of stem cell factor (Prospec)/ml, and 3 IU of erythropoietin/ml. From day 8 through day 14, the cells were cultured in the same medium without hydrocortisone or IL-3.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol from 250 ng total RNA (Affymetrix GeneChip 3' IVT Express kit Instruction Manual, P/N 702646 Rev. 5).
 
Hybridization protocol Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Perfect Match Peg Arrays using the Affymetrix Gene Atlas system (software version 1.0.4.267).
Scan protocol Arrays were scanned using the Affymetrix Gene Atlas system.
Description gene expression data from 5 µM TC treated, day 8 in vitro differentiated human erythroid cells
Data processing Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.15.0. RMA was used to normalize the data and fit log2 transformed expression values
 
Submission date Nov 06, 2012
Last update date Feb 16, 2013
Contact name Lihong Shi
E-mail(s) shilh@med.umich.edu
Organization name University of Michigan
Street address 3608 BSRB, 109 Zina Pitcher Place
City Ann Arbor
ZIP/Postal code 48109
Country USA
 
Platform ID GPL13667
Series (1)
GSE42078 Expression data of differentiated human erythroid cells with or without Tranylcypromine (TC) treatment

Data table header descriptions
ID_REF
VALUE Log2 Transformed RMA

Data table
ID_REF VALUE
11715100_at 5.056962053
11715101_s_at 6.114217483
11715102_x_at 5.201076391
11715103_x_at 5.633778848
11715104_s_at 4.418770134
11715105_at 3.602343885
11715106_x_at 4.176293822
11715107_s_at 3.938042088
11715108_x_at 3.888026943
11715109_at 4.366837777
11715110_at 5.373105338
11715111_s_at 6.766767657
11715112_at 3.476554694
11715113_x_at 6.3383486
11715114_x_at 6.735988737
11715115_s_at 3.027751379
11715116_s_at 4.340231877
11715117_x_at 4.328564032
11715118_s_at 5.309714716
11715119_s_at 6.272600118

Total number of rows: 49386

Table truncated, full table size 1226 Kbytes.




Supplementary file Size Download File type/resource
GSM1032115_Engel_004.ga.cel.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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