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Protocols

BDGP specifications

Information


Unique identifier OMICS_22557
Name BDGP
Alternative name Berkeley Drosophila Genome Project
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster

Publication for Berkeley Drosophila Genome Project

BDGP citations

 (264)
library_books

Direct measurement of pervasive weak repression by microRNAs and their role at the network level

2018
BMC Genomics
PMCID: 5952853
PMID: 29764374
DOI: 10.1186/s12864-018-4757-z

[…] The gene annotation file was downloaded from the Ensembl database. RNA-seq reads were mapped to D. melanogaster Reference Genome (BDGP6.83) using tophat [] and transcripts’ expression value was quantified as “Fragments Per Kilobase of exon per Million fragments mapped” (FPKM) using Cufflinks []. […]

call_split

Intronic PAH gene mutations cause a splicing defect by a novel mechanism involving U1snRNP binding downstream of the 5’ splice site

2018
PLoS Genet
PMCID: 5933811
PMID: 29684050
DOI: 10.1371/journal.pgen.1007360
call_split See protocol

[…] ng the Human Splicig Finder (HSF) program (http://www.umd.be/HSF3/) [], MaxEntScan software (http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html) [], the BerkeleyDrosophila Genome Project (BDGP) splice prediction tool (http://www.fruitfly.org/seq_tools/splice.html) [] and ESEFinder 3.0 software (http://rulai.cshl.edu) []. […]

call_split

Cooperative STAT/NF κB signaling regulates lymphoma metabolic reprogramming and aberrant GOT2 expression

2018
Nat Commun
PMCID: 5904148
PMID: 29666362
DOI: 10.1038/s41467-018-03803-x
call_split See protocol

[…] (Illumina, San Diego, CA, USA). Libraries were sequenced in single end mode for 100 cycles on an Illumina HiSeq 2000.We concatenated the genomes of Homo sapiens (GRCh38) and D. melanogaster (Ensembl BDGP5), and mapped all sequence libraries against this concatenated genome using TopHat version 2.0.13, indicating an unstranded sequencing protocol (library-type fr-unstranded) and default settings f […]

library_books

A Distalless responsive enhancer of the Hox gene Sex combs reduced is required for segment and sex specific sensory organ development in Drosophila

2018
PLoS Genet
PMCID: 5909922
PMID: 29634724
DOI: 10.1371/journal.pgen.1007320

[…] Genomic sequences homologous to the D. melanogaster ScrE sequence were analyzed via Blat using the D. melanogaster genome (BDGP release 6 + ISO1 MT/dm6) at the UCSC Genome Browser website. […]

call_split

Integrated biology approach reveals molecular and pathological interactions among Alzheimer’s Aβ42, Tau, TREM2, and TYROBP in Drosophila models

2018
Genome Med
PMCID: 5875009
PMID: 29598827
DOI: 10.1186/s13073-018-0530-9
call_split See protocol

[…] manufacturer’s protocol (Illumina).Single-ended RNA-seq data were generated with the Illumina HiSeq 2500 platform following the Illumina protocol. The raw sequencing reads were aligned to fly genome BDGP6 using star aligner (version 2.5.0b). Following read alignment, featureCounts [] was used to quantify the gene expression at the gene level based on Ensembl gene model. Genes with at least 5 read […]

library_books

Detection of mutations in MYOC, OPTN, NTF4, WDR36 and CYP1B1 in Chinese juvenile onset open angle glaucoma using exome sequencing

2018
Sci Rep
PMCID: 5852028
PMID: 29540704
DOI: 10.1038/s41598-018-22337-2

[…] sults were mapped against UCSC hg19 by Burrows-Wheeler Aligner.Exome sequencing results were filtered with the following steps: (1) Noncoding variants without altering splicing sites predicted by the Berkeley Drosophila Genome Project (available in the public domain at http://www.fruitfly.org/seq_tools/splice.html) were excluded; (2) The synonymous variants without altering splicing sites were rem […]


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BDGP institution(s)
Department of Embryology, Howard Hughes Medical Institute Research Laboratories, Carnegie Institution of Washington, Baltimore, MD, USA; Department of Molecular and Cellular Biology, Howard Hughes Medical Institute Research Laboratories, University of California, Berkeley, CA, USA
BDGP funding source(s)
Supported by a genome center grant (P50NIHHG750) from the National Institutes of Health and Howard Hughes Medical Institute Investigators.

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