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| Status |
Public on Nov 09, 2022 |
| Title |
Transcriptomic and chromatin accessibility analyses of porcine alveolar macrophages exposed to Fumonisin B1 |
| Organism |
Sus scrofa |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Fumonisin B1 (FB1) is a mycotoxin that poses a great threat to agricultural production and human and animal health. However, the molecular mechanism underlying the cytotoxic effect of FB1 to mammals has not been systematically elucidated. Here, we utilized the porcine alveolar macrophage cell line 3D4/21 as model, and applied RNA sequencing (RNA-seq) to analyze the genome-wide transcriptional alterations of mRNA, lncRNA, circRNA and miRNA before and after exposure to FB1 in six samples. To further reveal the underlying regulatory mechanism, we applied Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to determine the genome-wide chromatin accessibility alterations in response to FB1-induced cytotoxicity. We anticipate that this dataset will serve as valuable resource for clarifying the transcriptional and regulatory mechanism underlying the cytotoxic effect of FB1, and facilitate the identification of the key genes and signaling pathways contributing to cellular response to FB1 exposure.
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| Overall design |
We analyzed the transcriptional alterations of mRNA, lncRNA, circRNA and miRNA in porcine alveolar macrophages before and after exposure to FB1 using RNA-Seq. Using ATAC-seq technology, we determined changes in genome-wide chromatin accessibility in porcine alveolar macrophages in response to FB1-induced cytotoxicity.
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| Contributor(s) |
Jin J, Jiang J, Wu Z, Huang R, Sun M, Bao W |
| Citation(s) |
36330331, 36552567 |
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| Submission date |
Dec 06, 2021 |
| Last update date |
Jan 11, 2023 |
| Contact name |
靳 健 |
| E-mail(s) |
jiayao.jiang7@gmail.com
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| Phone |
18860895953
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| Organization name |
扬州大学
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| Street address |
扬州大学荷花池校区
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| City |
扬州 |
| State/province |
江苏 |
| ZIP/Postal code |
225000 |
| Country |
China |
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| Platforms (2) |
| GPL19176 |
Illumina HiSeq 2500 (Sus scrofa) |
| GPL22475 |
Illumina HiSeq 4000 (Sus scrofa) |
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| Samples (16)
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| GSM5719323 |
alveolar macrophage, NC-1, ATAC-seq |
| GSM5719324 |
alveolar macrophage, NC-2, ATAC-seq |
| GSM5719325 |
alveolar macrophage, NC-3, ATAC-seq |
| GSM5719326 |
alveolar macrophage, FB1-1, LncRNA-seq |
| GSM5719327 |
alveolar macrophage, FB1-2, LncRNA-seq |
| GSM5719328 |
alveolar macrophage, FB1-3, LncRNA-seq |
| GSM5719329 |
alveolar macrophage, NC-1, LncRNA-seq |
| GSM5719330 |
alveolar macrophage, NC-2, LncRNA-seq |
| GSM5719331 |
alveolar macrophage, NC-3, LncRNA-seq |
| GSM5719332 |
alveolar macrophage, FB1-1, miRNA-seq |
| GSM5719333 |
alveolar macrophage, FB1-2, miRNA-seq |
| GSM5719334 |
alveolar macrophage, NC-1, miRNA-seq |
| GSM5719335 |
alveolar macrophage, NC-2, miRNA-seq |
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| Relations |
| BioProject |
PRJNA786598 |
| SRA |
SRP349439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE190291_LncRNA_CodeGenesExpression_fpkm.csv.gz |
542.4 Kb |
(ftp)(http) |
CSV |
| GSE190291_RAW.tar |
5.9 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE190291_all_mirna_tpm.xlsx |
151.9 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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