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| Status |
Public on Jan 13, 2021 |
| Title |
Elucidation of the open chromatin regions in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus, using ATAC-Seq |
| Organism |
Bos taurus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). The objective of this study was to elucidate the chromatin regions which were differentially open in the bronchial lymph nodes (BLN) of dairy calves experimentally challenged with BRSV, relative to unchallenged control calves. Holstein-Friesian calves were either challenged with BRSV inoculum (n=12) or mock challenged with PBS (n=6). Calves were euthanised on day 7 post-challenge. ATAC-Seq libraries were prepared from fresh BLN tissues and sequenced (75 bp paired-end). Sequence reads were aligned to the UMD3.1 reference genome and peak calling (q < 0.01) was performed with MACS2, employing the BAMPE model. Using Diffbind, 9,144 and 5,096 differentially accessible peaks were identified between BRSV challenged and control calves (P < 0.05, FDR < 0.05) using DeSeq2 and EdgeR, respectively. There were 169 and 110 genes previously found to be differentially expressed using RNA-Seq located within or up to 2kb upstream of the differentially accessible peaks identified by the DeSeq 2 and EdgeR analyses, respectively. There were 237 differentially accessible peaks positioned within 40 previously identified susceptibility loci for BRD. These open chromatin regions are likely involved in the gene transcriptional and regulatory response to infection by BRSV.
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| Overall design |
Examination of a single tissue type (broncial lymph node) in two different treatment groups, BRSV challenged calves (n=12) and control calves (n=6)
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| Contributor(s) |
Johnston D, Kim J, Taylor JF, Earley B, McCabe MS, Lemon K, Duffy C, McMenamy M, Cosby SL, Waters SM |
| Citation(s) |
33407093 |
| Submission date |
Apr 03, 2020 |
| Last update date |
Jan 13, 2021 |
| Contact name |
Dayle Johnston |
| Organization name |
Teagasc
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| Department |
Animal and Bioscience Research Department
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| Lab |
Teagasc Grange
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| Street address |
AGRIC
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| City |
Dunsany |
| State/province |
Ireland |
| ZIP/Postal code |
C15 PW93 |
| Country |
Ireland |
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| Platforms (1) |
| GPL23055 |
Illumina NextSeq 500 (Bos taurus) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA622966 |
| SRA |
SRP255167 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE148056_RAW.tar |
16.9 Mb |
(http)(custom) |
TAR (of NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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