|
| Status |
Public on Sep 07, 2023 |
| Title |
DNA methylation-environment interactions in the human genome |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
This project uses the massively parallel reporter assay, mSTARR-seq (Lea et al., 2018) to simultaneously test for both enhancer-like activity and DNA methylation-dependent enhancer activity across nearly the entire human genome. We assessed enhancer activity at almost all CpG sites profiled either on the commonly used Illumina Infinium MethylationEPIC array or via reduced representation bisulfite sequencing. Experiments were performed in K562 and HepG2 cells.
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| Overall design |
In this data set, 6 replicate flasks of K562 cells were treated for 6 hours with each of the following treatments: dexamethasone (1 uM), IFNA2b (2,000U/ml), or vehicle control (media). Cells were then collected for mRNA-Seq to assess the endogenous gene expression response of K562 cells to treatment.
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| |
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| Contributor(s) |
Johnston RA |
| Citation(s) |
37293015, 38407202 |
| |
| Submission date |
Jan 11, 2023 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Rachel A Johnston |
| E-mail(s) |
racheljohnston7@gmail.com
|
| Organization name |
Duke University
|
| Department |
Evolutionary Anthropology
|
| Lab |
Jenny Tung
|
| Street address |
130 Science Dr, Rm 108 Biological Sciences
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (18)
|
| GSM6928204 |
L31416_K562_endogenous_RNA_Dex_replicate1 |
| GSM6928205 |
L31417_K562_endogenous_RNA_IFNA_replicate1 |
| GSM6928206 |
L31418_K562_endogenous_RNA_baseline_replicate1 |
| GSM6928207 |
L31419_K562_endogenous_RNA_Dex_replicate2 |
| GSM6928208 |
L31420_K562_endogenous_RNA_IFNA_replicate2 |
| GSM6928209 |
L31421_K562_endogenous_RNA_baseline_replicate2 |
| GSM6928210 |
L31422_K562_endogenous_RNA_Dex_replicate3 |
| GSM6928211 |
L31423_K562_endogenous_RNA_IFNA_replicate3 |
| GSM6928212 |
L31424_K562_endogenous_RNA_baseline_replicate3 |
| GSM6928213 |
L31425_K562_endogenous_RNA_Dex_replicate4 |
| GSM6928214 |
L31426_K562_endogenous_RNA_IFNA_replicate4 |
| GSM6928215 |
L31427_K562_endogenous_RNA_baseline_replicate3 |
| GSM6928216 |
L31428_K562_endogenous_RNA_Dex_replicate5 |
| GSM6928217 |
L31429_K562_endogenous_RNA_IFNA_replicate5 |
| GSM6928218 |
L31430_K562_endogenous_RNA_baseline5 |
| GSM6928219 |
L31431_K562_endogenous_RNA_Dex_replicate6 |
| GSM6928220 |
L31432_K562_endogenous_RNA_IFNA_replicate6 |
| GSM6928221 |
L31433_K562_endogenous_RNA_baseline_replicate6 |
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| Relations |
| BioProject |
PRJNA922950 |
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