Search for Data Metadata
| Data name ⇅ | Database name ⇅ | DOI ⇅ | Description of data contents ⇅ | Data acquisition method ⇅ | Data analysis method ⇅ | Data detail |
|---|---|---|---|---|---|---|
| Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile | Dicty_cDB | 10.18908/lsdba.nbdc00419-002 |
Contig sequences of cDNA sequences of Dictyostelium discoideum and their annotation (amino acid sequence and results of homology search (with target DBs: contig sequence-DB, DNA-DB and protein-DB)). Contig sequences are obtained by assemblying 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program Phrap (http://www.phrap.org/index.html). Link to the list of clones constituting the contig, the information on its mapping to the genome mapped to genome sequence and the list of top 10 hits in the results of homology search are provided. Also, the number of clones constituting the contig in each library is given for five developmental stages and 14 different libraries. Library-specific clones can be searched. The data are given in a CSV format text file. |
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EST sequences were assembled by Phrap. |
Data detail
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| EST sequences and their annotation (amino acid sequence and results of homology search) | Dicty_cDB | 10.18908/lsdba.nbdc00419-001 |
Sequences of cDNA clones of Dictyostelium discoideum and their annotations (amino acid sequence, homology search results (with target DBs: dicty EST-DB, DNA-DB and protein-DB)). Links to the Atlas database (http://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html), which is the database of images depicting localization of clones in Dictyostelium discoideum, the National BioResource Project (http://www.nbrp.jp/) and the dictyBase (http://dictybase.org/) are provided. Link to the table of contigs containing EST sequences is also provided. For each clone, the following four categories are established: 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence. If both 5' EST sequence and 3' EST sequence are available, the treatment to ligate the 5' EST sequence to the 3' EST sequence is peformed to generate a sequence connecting the two sequences with ten pieces of hyphen. If an overlapped region exists between the two sequences, the sequence obtained by overlapping is considered as a full-length sequence. For some clones that do not allow overlapping, the full-length is obtained by sequencing the gap region. F, Z, P and E are added to the end of the Clone ID to identify 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence. For each clone, these sequences are stored on a single line. Among these sequences, one sequence is selected as the representative sequence by prioritizing full-length cDNA sequence, 5' EST-3'EST-ligated sequence, 5' EST sequence and 3' EST sequence in this order, and the BLAST-based homology search is performed. Search is performed by the blastn search against clone sequences of dicty_cDB, the DNA sequence in public database, and blastx search against the protein sequence in public database, and then the top 10 hit information is stored. CSV format text file. |
Capillary sequencer |
Clones obtained from 11 different cDNA libraries originating from five developmental stages were sequenced. |
Data detail
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| Literature list concerning differentiation and activation of macrophage and pathways found in the literature | DMPD | 10.18908/lsdba.nbdc00558-001 |
Literature list concerning curated differentiation and activation of macrophage. The list is a CSV format text file. |
Search on PubMed |
The curator reads the literature, and converts the contents into a pathway in the CSML format by using the Cell Illustrator Online (CIO). |
Data detail
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| Pathway data concerning differentiation and activation of macrophage | DMPD | 10.18908/lsdba.nbdc00558-002 |
Pathways concerning differentiation and activation of macrophage extracted from the literature list in the CSML format, which is an XML format. One CSML file to an article. |
Pathways are extracted from each paper in the above literature list in the CSML format, which is an XML format. |
The curator reads the literature, and converts the contents into a pathway in the CSML format by using Cell Illustrator Online (CIO). |
Data detail
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| Solubility | eSOL | 10.18908/lsdba.nbdc00440-001 |
The solubilities of individual proteins were evaluated by using a cell-free translation system (PURE system) which is chaperone-free.
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After the protein synthesis with [35S]methionine, an aliquot was withdrawn as the total fraction, and the remainder was centrifuged at 21,600 × g for 30 min. Both the total and supernatant fractions were separated by SDS-PAGE, and the band intensities were quantified by autoradiography. |
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Data detail
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| Data name | Database name | DOI | Description of data contents | Data acquisition method | Data analysis method | Data detail |