開題第3組田豐-報(bào)告

1、 田豐 10101024指導(dǎo)教師 李萍 高歌Analysis of long intergenic non-coding RNAs (LincRNAs)involved in neural development of hESC目錄1234BackgroundMethodProgressViability1Background-lncRNAs= 0.1 in every sample under the same conditionLength 200 ntCPC: non-codingIntergenic3Progress2013.10LincRNA2013.11RNA-seq2013.12

2、2014.32014.42014.5DE geneslincRNAs2013.10.2013.12 Learn about lincRNAs 2014.12.2014.02 RNA-seq analysis software2014.02.2014.04 RNA-seq data genome analysis2014.04.2014.05 LincRNA identification2014.05.2014.06 paper3Progress1. Data (GSE20301 in GEO)Dynamic transcriptomes during neural differentiatio

3、n of hESC6 samples:hESC_A; N1_A; N2_A; N3_A; hESC_B; N2_B3 sequencing methods:Single readsPaired readsLong reads (missing)The analysis for New data is on my plan after GSE20301.3Progress2. AnalysisThe density of genes in approach A1 fpkm:continued to decline, which may have functions related with pl

4、uripotency.Peaks num.H, N1, N2 have 2 peaksN3 just have 1 peak 3Progress2. AnalysisH-AN1-AN2-AN3-AH-A-6st1st3rdN1-A2103-2nd4thN2-A43793414-5thN3-A337730002353-I got 18626 differential genes for approach AH-A:N1-AN1-A:N2-AN2-A:N3-A210334142353+702 (9)1948 (30)1343 (8)-1401(27)1466 (37)1010 (39)Ratio0

5、.5011 1/1.99571.32871.3297H-A:N2-A mostH-A:N1-A ratio1 in H-A:N1 Maintain pluripotency1.32871.3297 specific genes may have some important functions.3Progress2. AnalysisDifferential genes TTLL10(+) and VWA1(-) and their isoformsTTLL10: chr1 polyglycylase nucleosome H1VWA1: chr1 cartilage structure an

6、d function4ViabilityPapers about lincRNAsSequencing dataLinux programming skillsRNA-seq analysis process5ReferenceDerrien T., et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22(9): 1775-1789.Yong He, et al. (

7、2014). Long noncoding RNAs: Novel insights into hepatocelluar carcinoma. Cancer Letters 344(1):20-7Jia Qian Wua, et al. (2010). “Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.” PNAS 107(11): 5254-5259Julieta Apre

8、a, et al. (2013). “Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment.” The EMBO Journal 9ThanksTianFengIs it ture?Compare lincRNAs with those in published paperIyengar B R, Choudhary A, Sarangdhar M A, et al. Non-coding RNA interact to regulate neuronal development and functionJ. Frontiers in cellular neuroscience, 2014, 8.Ng S Y, Johnson R, Stanton L W. Human long noncoding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factorsJ. T