DBTMEE
Database of Transcriptome in Mouse Early Embryos


Annotations

  • RefFlat (used in V2.0)
  • RefLink (used in V2.0)
  • RefSeq GTF file (used in V2.0)
  • RefFlat (used in V1.0)
  • RefLink (used in V1.0)
  • Map of JASPAR motifs to TRANSFAC DB: [DL]
  • TSS positions



  • Sequenced Reads

  • csfastq (Stage_Replica_F3.csfastq.bz2 format):  [DL (46GB)] [md5]
       (%>tar xfvz filename[directory]
  • One-cell embryos treated with alpha-amanitin (Illumina fastq):  [directory]
  • Raw sequenced data: DRA001066



  • Mapped Reads

  • BAM file is downloadable from [directory]



  • Tables

  • All tables used in DBTMEE: [DL] [md5]
       (%>tar xfvz filename), NOTE: TSV files are tab-delimited text files. Users can import these to Excel sheets.
       [Description for tables]

  • UPDATE [2014.2.24]
       Cuffdiff (ver:2.1.1) was used:  [DL]
       Expression profile:  [DL]
       (%>tar xfvz filename)

       NOTE:  this "known_genes.tar.gz" file includes;
        "gene_expression.dat" - tab-delimited text file including FPKMs at Sperm, Oo-4C, p1C, and p4C
        "gene_expression_diff_stat.dat" - tab-delimited text file including all the pairwise statistical tests
        "xxxxx.ps" - postscript files plotting the FPKM distribution
        "xxxxx.pdf" - PDF files converted from the postscript files
        "gene_expression_diff_stat.dat_3fpkm_2fc.pdf" - particularly, this PDF shows differentially expressed genes (FDR<0.05, FC>2.0, FPKM>3.0)
        "gene_expression_diff_stat.dat_3fpkm_2fc.list.dat" - the complete list of differentially expressed genes

  • UPDATE with ES and iPS cells (GSE53212) [2014.4.20]
       Cuffdiff (ver:2.1.1) was used:  [DL]
       Expression profile:  [DL]
       (%>tar xfvz filename)

       NOTE:  this "known_genes.tar.gz" file includes;
        "gene_expression.dat" - tab-delimited text file including FPKMs at Sperm, Oo-4C, p1C, and p4C
        "gene_expression_diff_stat.dat" - tab-delimited text file including all the pairwise statistical tests
        "xxxxx.ps" - postscript files plotting the FPKM distribution
        "xxxxx.pdf" - PDF files converted from the postscript files
        "gene_expression_diff_stat.dat_3fpkm_2fc.pdf" - particularly, this PDF shows differentially expressed genes (FDR<0.05, FC>2.0, FPKM>3.0)
        "gene_expression_diff_stat.dat_3fpkm_2fc.list.dat" - the complete list of differentially expressed genes



  • Supplements for DBTMEE V1.0

  • Figure_S4.pdf: Gene expression patterns (25 clusters)
  • raw data of clustering: [ZIP] [TAR.GZ] [md5]
  • Figure_S6.pdf: TF-gene network
  • Network file in cytoscape 3.0 format: [DL]
  •  

    Cross Search: 

    Gene Search: 

    BioGPS: 


    Please cite  Nucl. Acids Res. 43(D1):D771-D776, 2015

    [What's New]
  • SRA collection from recent publications (2016.04.01)
  • New publication for DBTMEE [Nucleic Acids Research] (2015.01.28)
  • Ensembl ID is now searchable via "Gene Search" page (2014.11.14)
  • DBTMEE ver2.0 is now available (2014.06.30)
  • Updated expression profile is now available (2014.04.20)
  • Updated expression profile is now available (2014.02.24)
  • LLM (Log-linear Modeling) now available (2013.12.05)
  • Alpha-amanitin treated one-cell embryos DRA001066 added (2013.10.22)
  • DDBJ accession number is DRA001066 (2013.07.04)
  • Gene card updated (2013.06.25)
  • PPI data, proteomics data, microarray added (2013.04.24)
  • RNA-seq datasets (Illumina, SOLiD single cell) added (2013.03.22)
  • Parthenogenesis RNA-seq data added (2012.12.01)
  •