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Transcriptome Profiling of Murine and Human ES Cells Identifies Divergent Paths Required to Maintain the Stem Cell State

MPSS stem cell database (prototype version) is an effort between two groups : Cloning and Sequencing Group and Stem Cell Group. The MPSS stem cell database is a web based database that is being developed at GIS for rapid and reliable display of MPSS data in the genome context. This browser displays MPSS signatures and transcripts mapped to any chosen region of the genome. At this point only the prototype version is available. We will continue to provide more functionality in the next version in the near future. The database for the browser is build on top of MySQL and utilizes human (hg17) and mouse genome (mm5) sequences. Annotation tables were downloaded from UCSC Golden Path (genome.ucsc.edu). To generate MPSS signature mapping to the genome, all 20 bp signatures were mapped with 100% identity to its position in the genome and separately by numbers of specific mapping locations. Using the genome context where the signatures mapped, proper mRNA and transcript information were assigned to each signature. The graphical display is adapted from UCSC genome browser and can be accessed through the link at chromosomal location. The expression profiling for each transcript can be viewed by clicking the signatures annotated to specific mRNA by normalized tpm and digital northern pattern.

For further question, please contact: Dr. Wei, ChiaLin Cloning and Sequencing Group weicl@gis.a-star.edu.sg

MPSS Stem Cell Database

Sort By Year | First Author | Publication Title Publications from 2005 1. Xu XQ, Emerald BS, Goh EL, Kannan N, Lance D MILLER, Gluckman PD, Edison Tak-Bun LIU, Lobie PE (2005) "Gene expression profiling to identify oncogenic determinants of autocrine human growth hormone (hGH) in human mammary carcinoma Contact Author:    Supplemental dataset 1 - Genes regulated by the exogenous hGH using human 19 K Oligonucleotide arrays Supplemental dataset 2 2. Chia Lin WEI, Ken Wing Kin SUNG, Kuo Ping CHIU, Ang Chin Chin, Shahab Atif, Ridwan Azmi, Wong Chee Hong, Edison Tak-Bun LIU, Yijun RUAN (2005) "Gene identification signature (GIS) analysis for transcriptome analysis and genome annotation Contact Author:    Download the latest protocol Publications from 2004 1. Chia Lin WEI, Kuo Ping CHIU, Chee Hong Wong, Chin Chin Ang, Edison Tak-Bun LIU, Yijun RUAN (2004) "5' Long serial analysis of gene expression (LongSAGE) and 3' LongSAGE for transcriptome characterization and genome annotation Contact Author:    Detailed 5'LongSAGE and 3'LongSAGE protocols Table 3: summary of RT-PCR validation results, and lists of all 5' and 3' LongSAGE tags 2. Lance D MILLER, McPhie P, Suzuki H, Kato Y, Edison Tak-Bun LIU, Cheng S-Y (2004) "Multi-tissue gene expression analysis in a mouse model of thyroid hormone resistance Contact Author:    Table of all redundant microarray probes and their average expression ratio measurements. Comprehensive filtered gene list of average expression ratios. Responsive genes known to be modulated by T3. Genes differentially expressed in the heart of iT3 and/or RTH mice. Genes differentially expressed in the white adipose tissue (WAT) of iT3 and/or RTH mice. Genes differentially expressed in the cerebellum of iT3 and/or RTH mice. Raw comprehensive expression ratios. Hierarchical clustergram of 2.0r outlier genes with full annotation. 3. Christopher WONG, Albert, T.J, Vinsensius Berlian VEGA, Norton, J.E., Cutler, D.J., Richmond, T.A, Lawrence STANTON, Edison Tak-Bun LIU, Lance D MILLER (2004) "Tracking the Evolution of the SARS Coronavirus using Rapid, High-throughput, High-density Resequencing Arrays.. Contact Author:    Supplementary Data Links to other materials: Supplementary Data Publications from 2003 1. Sotiriou C, McShane L.M., Korn E.L., Long M. Philip, Jazaeri A., Martiat P., Fox S.B., Harris A.L., Edison Tak-Bun LIU (2003) "Breast cancer classification and prognosis based on gene expression profiles from a population-based study.. Contact Author:    Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 TABLE 1: Patient s Demographics supplementary TABLE 3 706-probe e lements supplementary TABLE 4 485 sur vival gene list supplementary TABLE 5 ER status supplementary TABLE 6 GRADE supplementary TABLE 8 logs row DATA TABLE 9 row intesi ties Channel 635 2. Yijun RUAN, Chia Lin WEI, Ling Ai Ee, Vinsensius Berlian VEGA, Thoreau Herve, Su Yun Se Thoe, Chia Jer-Ming, Kuo Ping CHIU, Lim Landri, Zhang Tao, Chan Kwai Peng, Lynette Oon Lin Ean, Ng Mah Lee, Leo Yee Sin, Lawrence STANTON, Long M. Philip, Edison Tak-Bun LIU (2003) "Comparative full-length genome sequence analysis of 14 SARS coronavirus isolates and common mutations associated with putative origins of infection.. Contact Author:   Dr Yijun RUAN SIN2500 sequence.doc SIN2677 sequence.doc SIN2679 sequence.doc SIN2748 sequence.doc SIN2774 sequence.doc Supplementary data 1, 14 SARS sequences alignment.pdf Supplementary data 2, SARS sequence variation.pdf Supplementary figure, sequence variation and location.pdf Supplementary material, correspondence significance.pdf Publications from 2002 1. Lance D MILLER, Long PM, Wong L, Mukherjee S, McShane LM, Edison Tak-Bun LIU (2002) "Optimal gene expression analysis by microarrays Contact Author:    Download