1.课程名称：水产养殖基础前沿课I（课程编号：0121303）

2.主讲教师：刘占江教授

美国奥本大学渔业水产水生生物学院基因组学研究室主任

3.授课内容：

Lecture1. Transcriptome and transcriptomics: Will cover the concepts of genome, transcriptome, and trancriptomics

Lecture2. Technologies for transcriptome studies: Will cover EST sequencing, SAGE, SSH, microarrays, RNA-Seq, etc.

Lecture3. Comparison of various transcriptome analysis technologies: Pros and cons

Lecture4. Application of RNA-Seq technologies in aquaculture

Lecture5. Bulk segregant analysis and Bulk segregant RNA-Seq (BSR-Seq)

Lecture 6. Pervasive transcription: miRNA, lncRNA, etc

Examination: 50 multiple choices, 2 points each

4. 课程要求：

• from the following list:

(1) Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Khoo L, Kucuktas H, Peatman E, Liu Z. Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics. 2012 Nov 5;13:595. doi: 10.1186/1471-2164-13-595. PubMed PMID: 23127152; PubMed Central PMCID: PMC3582483.

(2) Sun F, Peatman E, Li C, Liu S, Jiang Y, Zhou Z, Liu Z. Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Dev Comp Immunol. 2012 Sep;38(1):169-80. doi: 10.1016/j.dci.2012.05.006. Epub 2012 Jun 2. PubMed PMID: 22669032.

(3) Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol. 2012 May;32(5):816-27. doi: 10.1016/j.fsi.2012.02.004. Epub 2012 Feb 17. PubMed PMID:  22366064.

(4) Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 2011 Jan 21;12:53. doi: 10.1186/1471-2164-12-53. PubMed PMID: 21255432; PubMed Central PMCID: PMC3033819.

(5) Wang R, Sun L, Bao L, Zhang J, Jiang Y, Yao J, Song L, Feng J, Liu S, Liu Z.  Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish. BMC Genomics. 2013 Dec 30;14:929. doi: 10.1186/1471-2164-14-929. PubMed  PMID: 24373586; PubMed Central PMCID: PMC3890627.

(6) Sun F, Liu S, Gao X, Jiang Y, Perera D, Wang X, Li C, Sun L, Zhang J, Kaltenboeck L, Dunham R, Liu Z. Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome. PLoS One. 2013 Jul 12;8(7):e68452.  doi: 10.1371/journal.pone.0068452. Print 2013. PubMed PMID: 23874634; PubMed Central PMCID: PMC3709890.

(7) Liu S, Wang X, Sun F, Zhang J, Feng J, Liu H, Rajendran KV, Sun L, Zhang Y, Jiang Y, Peatman E, Kaltenboeck L, Kucuktas H, Liu Z. RNA-Seq reveals expression  signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish. Physiol Genomics. 2013 Jun 17;45(12):462-76. doi: 10.1152/physiolgenomics.00026.2013. Epub 2013 Apr 30. PubMed PMID: 23632418.

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研究生院

水产与生命学院

2015年10月23日