随着新一代高通量测序技术的快速发展，在准确度大大提高的前提下,进一步降低测序成本。由此不断产生出巨量的分子生物学数据，这些数据有着数量巨大、关系复杂的特点，以至于不利用计算机根本无法实现数据的存储和分析。随着生物信息学作为新兴学科迅速蓬勃发展，正在改变人们研究生物医学的传统方式，高通量测序技术以及数据分析技术已成为探索生物学底层机制和研究人类复杂疾病诊断、治疗及预后的重要工具，广泛应用于生命科学各个领域，是21世纪生命科学与生物技术的重要战略前沿和主要突破口。为进一步推动我国生物信息学特别是基因组学的发展，提高从业人员的技术水平，由 北京中科云畅应用技术研究院与中科院北京基因组研究所基因组科学与信息重点实验室 联合举办“高通量测序深度应用”高级培训班，由北京中科润开生物科技有限公司具体承办，相关事宜通知如下：

一、培训特点及目标：

培训立足于最新技术和工具，强调融汇贯通，强调综合应用；

“采用互动式教学，讨论式授课，案例试学习的授课模式”

会议邀请的主讲专家都是有理论和实践经验的研究人员，

学员通过与专家的直接交流，能够分享这些顶尖学术机构的研究经验和实验设计思路，在研究技术方面领悟更多。

二、培训对象:

大中专院校生物信息、生物计算、生命科学、医学、化学、农学、计算机科学、数学类专业的课程负责人、一线教师、教研室骨干人员、教学管理人员；科研单位从事生物、生命科学、微生物研究的相关人员；生物、医药、化学及相关企业的领导与技术骨干。

三、授课内容：

1. DNA测序技术的进化
   1. 第一代测序技术：Sanger测序原理
   2. 第二代测序技术：Illumina，454, Ion Torrent原理
   3. 第三代测序技术：PacBio, Hellicos原理
   4. 第四代测序技术: Oxford NanoPore原理
   5. 其他技术Hybridization based methods (NabSys)
2. High throughput Sequencing for various biological problems
   1. RNA Transcription
3. Chromatin Isolation by RNA Purification (ChIRP-Seq)
4.  Global Run-on Sequencing (GRO-Seq)
5. Ribosome Profiling Sequencing (Ribo-Seq)
6. RNA Immunoprecipitation Sequencing (RIP-Seq)
7. High-Throughput Sequencing of CLIP cDNA library (HITS-CLIP)
8. Crosslinking and Immunoprecipitation Sequencing (CLIP-Seq)
9. Photoactivatable Ribonucleoside–Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP)
10. Individual Nucleotide Resolution CLIP (iCLIP)
11. Native Elongating Transcript Sequencing (NET-Seq)
12. Targeted Purification of Polysomal mRNA (TRAP-Seq)
13. Crosslinking, Ligation, and Sequencing of Hybrids (CLASH-Seq)
14. Parallel Analysis of RNA Ends Sequencing (PARE-Seq)
15. Genome-Wide Mapping of Uncapped Transcripts (GMUCT)
16. Transcript Isoform Sequencing (TIF-Seq)
17. Paired-End Analysis of TSSs (PEAT)

2.2. RNA Structure

1. Selective 2’-Hydroxyl Acylation Analyzed by Primer Extension Sequencing (SHAPE-Seq)
2. Parallel Analysis of RNA Structure (PARS-Seq)
3. Fragmentation Sequencing (FRAG-Seq)
4. CXXC Affinity Purification Sequencing (CAP-Seq)
5. Alkaline Phosphatase, Calf Intestine-Tobacco Acid Pyrophosphatase Sequencing (CIP-TAP)
6. Inosine Chemical Erasing Sequencing (ICE)
7. m6A-Specific Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq)
   3.  Low-Level RNA Detection, Digital RNA Sequencing

1. Whole-Transcript Amplification for Single Cells (Quartz-Seq)
2. Designed Primer–Based RNA Sequencing (DP-Seq)
3. Switch Mechanism at the 5’ End of RNA Templates (Smart-Seq)
4. Switch Mechanism at the 5’ End of RNA Templates Version 2 (Smart-Seq2)
5. Unique Molecular Identifiers (UMI)
6. Cell Expression by Linear Amplification Sequencing (CEL-Seq)
7. Single-Cell Tagged Reverse Transcription Sequencing (STRT-Seq)
   4.  Low-Level DNA Detection

1. Single-Molecule Molecular Inversion Probes (smMIP)
2. Multiple Displacement Amplification (MDA)
3. Multiple Annealing and Looping–Based Amplification Cycles (MALBAC)
4. Oligonucleotide-Selective Sequencing (OS-Seq)
5. Duplex Sequencing (Duplex-Seq)
   5.  DNA Methylation

1. Bisulfite Sequencing (BS-Seq)
2. Post-Bisulfite Adapter Tagging (PBAT)
3. Tagmentation-Based Whole Genome Bisulfite Sequencing (T-WGBS)
4. Oxidative Bisulfite Sequencing (oxBS-Seq)
5. Tet-Assisted Bisulfite Sequencing (TAB-Seq)
6. Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq)
7. Methylation-Capture (MethylCap)
8. Methyl-Binding-Domain–Capture (MBDCap)
9. Reduced-Representation Bisulfite Sequencing (RRBS-Seq)
   6.  DNA-Protein Interactions

1. DNase l Hypersensitive Sites Sequencing (DNase-Seq)
2. MNase-Assisted Isolation of Nucleosomes Sequencing (MAINE-Seq)
3. Chromatin Immunoprecipitation Sequencing (ChIP-Seq)
4. Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE-Seq)
5. Assay for Transposase-Accessible Chromatin Sequencing (ATAC-Seq)
6. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET)
7. Chromatin Conformation Capture (Hi-C/3C-Seq)
8. Circular Chromatin Conformation Capture (4-C or 4C-Seq)
9. Chromatin Conformation Capture Carbon Copy (5-C)
   7.  Sequence Rearrangements

1. Retrotransposon Capture Sequencing (RC-Seq)
2. Transposon Sequencing (Tn-Seq)
3. Translocation-Capture Sequencing (TC-Seq)
4. Data analysis （part 1）：data pre-processing
   1. evaluation of data quality 数据分析

Data format，fasta，fastq，quality value，gff3

1. 2. Data cleanup

Quality filter, trimmer, clipper

5. Data analysis （part 2）：reference free analyses，无参转录组分析
   1. Trinity de novo transcriptome assembly
   2. Analysis of Differential Expressed Gene （DEGs）
   3. Abundance estimation using RSEM
   4. Differential expression analysis using EdgeR
   5. Explore the results (cummerbund)
   6. MA plot, Volcano plot, False Discovery Rate (FDR)
   7. hierarchical two-way clustering, pairwise sample-distance, gene expression profiles.
5. Data analysis （part 3）：reference based analyses，有参转录组分析
   1. Mapping reads to the reference (tophat)
   2. Assemble mapped reads (cufflinks)
   3. Merge sample-specific assemblies (cuffmerge)
   4. Analysis of Differentially Expressed Gene （DEGs）
   5. Identify DEGs (cuffdiff)
   6. Explore the results (cummerbund)
6. Data analysis （part 4）：from gene list to gene function，基因功能注释
   1. File format for annotation information: GFF3
   2. Annotation
   3. Homology search (BLAST+/SwissProt/Uniref90)
   4. Protein domain identification (HMMER/PFAM)
   5. Protein signal peptide and transmembrane domain prediction (singalP/tmHMM)
   6. Comparing to currently curated annotation databases (EMBL Uniprot eggnog/GO)
   7. Enrichment analysis using DAVID
   8. Gene name batch viewer
   9. Gene functional classification
   10. Functional annotation chart
   11. Functional annotation clustering

Lab

Lab1: Connection to cloudlab using Putty

Lab2: File transfer between cloudlab and local computer using filezilla

Lab3: Linux commands

Lab4: Reads quality evaluation: fastqc

Lab5a: Reads quality control: fastx tool kit

Lab5b: Processing the mapping file: samtool

Lab6: Reference free analysis: Tuxedo package

Lab7: Reference based analysis: Trinity package

Lab8: Annotation: Trinnotate

Lab9: Enrichment analysis using DAVID

*实际授课内容，会根据参会学员反应的实际问题，进行更有针对性的讲解，欢迎大家随时反应平时在科研工做中遇到的问题。

四、主讲专家：

主讲专家来自 中国科学院、中国医学科学院 科研机构的高级专家，拥有丰富的科研及工程技术经验，长期从事生物领域国家重大项目研究，具有资深的技术底蕴和专业背景

五、颁发证书：

学员经培训考试合格后可以获得：

由北京中科云畅应用技术研究院颁发的生物信息培训班结业证书。（注：请学员提供 身份证复印件一张，正反面）