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Protocols

DictyBase specifications

Information


Unique identifier OMICS_03158
Name DictyBase
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/DictyBase

Taxon


  • Invertebrates
    • Dictyostelium discoideum

Maintainer


  • person_outline Petra Fey

Publications for DictyBase

DictyBase citations

 (47)
library_books

The Parkinson's disease associated protein DJ 1 plays a positive nonmitochondrial role in endocytosis in Dictyostelium cells

2017
PMCID: 5665451
PMID: 28819044
DOI: 10.1242/dmm.028084

[…] A BLAST at DictyBase (the international dictyostelid genomics resource at http://dictybase.org; ) was used to identify the homologue of human DJ-1 in the D. discoideum proteome using the protein sequence of huma […]

library_books

Extreme genome diversity in the hyper prevalent parasitic eukaryote Blastocystis

2017
PLoS Biol
PMCID: 5608401
PMID: 28892507
DOI: 10.1371/journal.pbio.2003769

[…] del (HMM) was created using HMMER version 3 [], including clear homologs from combinations of the following taxa: H. sapiens (NCBI, http://www.ncbi.nlm.nih.gov/), S. cerevisiae (NCBI), D. discoideum (dictyBase, http://dictybase.org/), Arabidopsis thaliana (NCBI), C. reinhardtii (Phytozome, http://www.phytozome.net/), P. sojae (JGI, http://www.jgi.doe.gov/), T. pseudonana (JGI), Naegleria gruberi ( […]

library_books

TRE5 A retrotransposition profiling reveals putative RNA polymerase III transcription complex binding sites on the Dictyostelium extrachromosomal rDNA element

2017
PLoS One
PMCID: 5391098
PMID: 28406973
DOI: 10.1371/journal.pone.0175729

[…] eads. To define the insertion sites, the pre-processed reads (pseudoreads, retrotransposon and tRNA/adapter part trimmed) were mapped to the Dictyostelium reference genome (version 05-13-2009; http://dictybase.org) using BLAT []. In addition, pseudoreads were mapped to the left arm of the rDNA palindrome as published in GenBank AY171066 []. To avoid false positive results we only allowed following […]

library_books

Vps13F links bacterial recognition and intracellular killing in Dictyostelium

2017
PMCID: 5484366
PMID: 28076662
DOI: 10.1111/cmi.12722

[…] s), kil1 (4 replicates), kil2 (3 replicates), phg1A (4 replicates), and vps13F (4 replicates) KO cells. 50 nt singe‐end reads were mapped to the Dictyostelium discoideum genome (2009, downloaded from dictybase) using tophat (version 2.0.13) and bowtie2 (version 2.2.4) softwares. As the RNASeq data is stranded, parameter library‐type was set to fr‐secondstrand. Multihits were not allowed, by using […]

library_books

Improved annotation with de novo transcriptome assembly in four social amoeba species

2017
BMC Genomics
PMCID: 5282741
PMID: 28143409
DOI: 10.1186/s12864-017-3505-0

[…] titutes the best approximation of the assembly of transcripts expressed in the RNA-seq sequencing data. The transcripts were aligned against the existing genome and coding DNA (cDNA) references (from Dictybase (D. discoideum) and SACGB [], (D. fasciculatum, D. lacteum and P. pallidum)) using BLAT. Any transcripts not matching the existing references were searched against the NCBI ‘nt’ database wit […]

call_split

The C Terminal SynMuv/DdDUF926 Domain Regulates the Function of the N Terminal Domain of DdNKAP

2016
PLoS One
PMCID: 5173251
PMID: 27997579
DOI: 10.1371/journal.pone.0168617
call_split See protocol

[…] d for library preparation. The library preparation and sequencing were performed at the CCG (Cologne Center for Genomics). The CLIP raw reads were aligned to the D. discoideum genome sequence (http://dictybase.org/) using Bowtie2 []. We counted reads associated with genomic features with the tophat2 program []. For peak finding we used Piranha (http://smithlabresearch.org/software/piranha/). […]

Citations

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DictyBase institution(s)
dictyBase and the Dicty Stock Center, Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
DictyBase funding source(s)
Supported by National Institutes of Health (NIH) [GM64426, GM087371, HG0022].

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