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| Status |
Public on Oct 31, 2014 |
| Title |
Transcription map of the Swine Leukocyte Antigen complex and comparative biology of MHCs among vertebrates |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by genome tiling array
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| Summary |
Tiling arrays have been reported as highly relevant tools to improve annotation and identify new transcripts in genome sequences. Our aim was to refine annotation of the Swine Leucocyte Antigen (SLA) complex, which is a gene dense region spanning 2.4 megabases on both sides of the centromere of chromosome 7 with many genes involved in immune response and inflammation. To date, one hundred and fifty-one SLA genes and pseudogenes have been characterized or predicted. A high-density tiling array was produced, which covered the entire Hp1a.0 haplotype sequence and partially the centromeric junction on the q-arm. The array contained 386,620 55-70-mer oligonucleotides designed on both strands and tiled on average every nine bases. It was used to compare the transcriptome of peripheral blood mononuclear cells (PBMCs) either mock-stimulated or stimulated with phorbol myristate acetate (PMA) and ionomycin for 24 hours. In both conditions, 19% of the probes were expressed among which 47% not previously annotated. In addition to the expected transcripts, segmentation analysis revealed new transcriptional architectures of previously annotated genes, a limited transcription activity in the centromeric junction and frequent transcription in antisense orientation. Differential expression of non-annotated transcripts was detected between non-stimulated and stimulated PBMCs, suggesting a regulatory role during immune cell activation. These results contribute to drawing an extensive transcription map of the SLA complex and to comparative functional mapping between mammals. This kind of approach can be applied to any candidate region of the pig genome in order to carry out a consistent functional annotation.
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| Overall design |
Two-condition experiment, PMA ionomycine stimulated PBMCs vs. Control PBMCs. Biological replicates: 1 control, and 1 PMA ionomycine stimulated from 4 animals independently grown and harvested. One replicate per array. Total 8 slides.
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| Contributor(s) |
Gao Y, Rogel-Gaillard C |
| Citation missing |
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| |
| Submission date |
Feb 14, 2012 |
| Last update date |
Oct 31, 2014 |
| Contact name |
Yu GAO |
| E-mail(s) |
gysino@gmail.com
|
| Organization name |
GABI-GIS
|
| Department |
Animal Genetics
|
| Lab |
GIS
|
| Street address |
INRA, BAT440
|
| City |
Jouy en Josas |
| ZIP/Postal code |
78350 |
| Country |
France |
| |
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| Platforms (1) |
| GPL9130 |
Sus scrofa Swine Leucocyte Antigen region Tiling Array 385K Nimblegen |
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| Samples (8)
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| GSM875808 |
Control 301166_6c600_1205 |
| GSM875809 |
PMA ionomycine stimulated 301158_3p600_1205 |
| GSM875810 |
PMA ionomycine stimulated 301160_4p600_1205 |
| GSM875811 |
PMA ionomycine stimulated 301162_5p600_1205 |
| GSM875812 |
PMA ionomycine stimulated 301167_6p600_1205 |
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| Relations |
| BioProject |
PRJNA151891 |
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