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| Status |
Public on Nov 15, 2006 |
| Title |
MiRNA Expression data from Tk6 cell treated with arsenic, gamma-IR, or grown under folate-deficiency |
| Platform organisms |
Homo sapiens; Mus musculus; Rattus norvegicus |
| Sample organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
Folate deficiency, arsenic exposure, and gamma-IR are known developmental toxicants and have carcinogenic effects. The mechanism by which IR is known, but the effect of arsenic or folate deficiency remains unclear. Their effect may be mediated by epigenetic alterations, leading to miRNA expression changes, and this experiment examined this hypothesis
We used microarrays to detail the miRNA expression profiles of TK6 cells treated with 2 uM sodium arsenite for 6 days, folate-deficient media for 6 days, or 2.5 Gy IR exposure either acutely at 4 hours post exposure or long-term at 6 days post exposure, as well as requiste controls, all in biological triplicate.
Keywords: exposure differences
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| Overall design |
TK6, were cultured in standard RPMI 1640 (Invitrogen Inc., Gaithersburg, MD) or folate-deficient RPMI 1640 (Invitrogen). Growth media was supplemented with 10% fetal bovine serum (Invitrogen) and 1% penicillin-streptomycin; dialyzed fetal bovine serum (Invitrogen) was added to the folate-deficient medium in order to eliminate folic acid in the serum. For controls, folate-deficiency, arsenic exposure, and 6-day ?-IR exposure groups, 106 cells were diluted into 50ml of appropriate growth media. For the 4-hour post-?-IR exposure group, 107 cells were diluted into 50ml of growth media. For the arsenic exposed group, sodium arsenite was added to the media to a concentration of 2 ?M. For the ?-IR exposure groups, cells were diluted and allowed to incubate for 4 hours prior to irradiation treatment, and were exposed at a dose rate of 86.76 rad/min to a final dose of 2.5 Gy using a Philips MGC-40 X-ray source. Following exposure, cells were returned to the incubator. After fours hours, the short-term post-??-IR exposure group was collected for RNA isolation, as well as a mock (control) group. All experimental and control conditions were performed in triplicate. For all other groups, cells were cultured for 6 days, with the media changed and renewed, with the appropriate treatment, on day 3.
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| Contributor(s) |
Marsit CJ, Eddy K, Kelsey KT |
| Citation(s) |
17108120 |
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| Submission date |
Oct 12, 2006 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Carmen J Marsit |
| E-mail(s) |
cmarsit@hsph.harvard.edu
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| Organization name |
Harvard School of Public Health
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| Department |
Genetics and Complex Diseases
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| Lab |
Kelsey
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| Street address |
665 Huntington Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL4411 |
Ambion Human_Mouse_Rat mirVANA miRNA Bioarray_1566V1 |
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| Samples (21)
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| GSM139806 |
IR treatment 4h timepoint, biological rep3 |
| GSM139807 |
IR treatment 6d timepoint, biological rep1 |
| GSM139808 |
IR treatment 6d timepoint, biological rep2 |
| GSM139809 |
IR treatment 6d timepoint, biological rep3 |
| GSM139810 |
No treatment control 4h, biological rep1 |
| GSM139811 |
No treatment control 4h, biological rep2 |
| GSM139812 |
No treatment control 4h, biological rep3 |
| GSM139813 |
No treatment control for As and IR 6d, biological rep1 |
| GSM139814 |
No treatment control for As and IR 6d, biological rep2 |
| GSM139815 |
No treatment control for As and IR 6d, biological rep3 |
| GSM139816 |
As treatment, biological rep3 |
| GSM139817 |
IR treatment 4h timepoint, biological rep1 |
| GSM139818 |
Folate deficient growth, biological rep1 |
| GSM139819 |
Folate deficient growth, biological rep2 |
| GSM139820 |
Folate deficient growth, biological rep3 |
| GSM139821 |
Cells grown in normal media control for folate deficiency, biological rep1 |
| GSM139822 |
Cells grown in normal media control for folate deficiency, biological rep2 |
| GSM139823 |
Cells grown in normal media control for folate deficiency, biological rep3 |
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| Relations |
| BioProject |
PRJNA97827 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE6020_RAW.tar |
730.0 Kb |
(http)(custom) |
TAR (of GPR) |
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