DBTMEE
Database of Transcriptome in Mouse Early Embryos

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DB status: OK
Last modified: 2024/03/24

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]
   NOTE:the file "PARK_v2/RNASEQ_MM9_gene_expression.fpkm.tsv" included "NR" refseq records, which causes slightly different FPKMs compared to those in "gene_expression.dat" at known_genes.tar.gz.

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] ("NR" RefSeq records were discarded)
   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]

 

Functional Analysis in silico, Human Genome Center, the University of Tokyo
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