|
| 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) |
[email protected]
|
| 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 |
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