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| Status |
Public on Dec 01, 2023 |
| Title |
High-throughput reporter assay for human genetic variants overlapping ATF4 binding sites |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Activating Transcription Factor 4 (ATF4) is a transcription factor that regulates cellular responses to nutrient deficiency, endoplasmic reticulum stress and oxidative stress. At the organism level, it is implicated in processes such as hematopoiesis, skeletogenesis, eye development, memory, muscle atrophy, and carbohydrate and lipid metabolism. Here, we carried out a massively parallel reporter assay (MPRA) to identify allelic regulatory effects of human genetic variants that reside in ATF4 binding sites identified in ChIP-Seq experiments.
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| Overall design |
Massively parallel reporter assay (MPRA) in HepG2 cells to analyze allelic regulatory effects.
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| Contributor(s) |
Örd T, Örd D, Örd T |
| Citation(s) |
37906604 |
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| Submission date |
Feb 13, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Tiit Örd |
| E-mail(s) |
tiit.ord@ut.ee
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| Organization name |
University of Tartu
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| Department |
Institute of Genomics
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| Street address |
Riia 23b/2
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| City |
Tartu |
| ZIP/Postal code |
51010 |
| Country |
Estonia |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (14)
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| GSM7041640 |
HepG2, control, rep 4 |
| GSM7041641 |
HepG2, control, rep 5 |
| GSM7041642 |
HepG2, tunicamycin, rep 1 |
| GSM7041643 |
HepG2, tunicamycin, rep 2 |
| GSM7041644 |
HepG2, tunicamycin, rep 3 |
| GSM7041645 |
HepG2, tunicamycin, rep 4 |
| GSM7041646 |
HepG2, tunicamycin, rep 5 |
| GSM7041647 |
Input plasmid library, rep 1 |
| GSM7041648 |
Input plasmid library, rep 2 |
| GSM7041649 |
Input plasmid library, rep 3 |
| GSM7041650 |
Input plasmid library, rep 4 |
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| Relations |
| BioProject |
PRJNA934357 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE225216_raw_count_matrix.tsv.gz |
428.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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