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Status
Public on Nov 01, 2012
Title
Custom NimbleGen 12-plex Batrachochytrium dendrobatidis Oligo Expression Array
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Batrachochytrium dendrobatidis Manufacturer
NimbleGen
Manufacture protocol
See manufacturer's website
Description
We designed a NimbleGen 12-plex microarray for Bd based on the publically available Bd genomes JAM81 (B. dendrobatidis Sequencing Project, Joint Genome Institute: http://genome.jgi-psf.org/Batde5/Batde5.download.ftp.html ) and JEL423 (B. dendrobatidis Sequencing Project, Broad Institute of Harvard and MIT: http://www.broadinstitute.org/annotation/genome/batrachochytrium_dendrobatidis ). The microarray contained 133,254 60-mer probes representing a possible 8,896 expressed transcripts (probe sets). Probe sets were defined as all probes that mapped to a single transcript, which in turn mapped to a single gene.
Submission date
Apr 10, 2012
Last update date
Nov 01, 2012
Contact name
Thomas Poorten
E-mail(s)
tom.poorten@gmail.com Organization name
UC Berkeley
Department
Environmental Science, Policy, and Management
Street address
54 Mulford Hall
City
Berkeley
State/province
CA
ZIP/Postal code
94720
Country
USA
Samples (12)
GSM911925 , GSM911926 , GSM911927 , GSM911928 , GSM911929 , GSM911930
Series (1)
GSE37135 Substrate-specific gene expression in the amphibian chytrid pathogen
Data table header descriptions ID Unique transcript ID, same as SEQ_ID as used in the .ndf file
JGI_Gene_ID Gene ID from the JGI Batrachochytrium dendrobatidis sequencing project
Broad_Gene_ID Gene ID from the Broad Batrachochytrium dendrobatidis sequencing project
Broad_Transcript_ID Transcript ID from the Broad Batrachochytrium dendrobatidis sequencing project
INTERPRO_1 Interpro Protein Domain (comma separated)
INTERPRO_2 Interpro Accession ID (comma separated)
INTERPRO_3 Interpro Description (semicolon separated)
GO_1 Gene Ontology Accession ID (comma separated)
GO_2 Gene Ontology Term (semicolon separated)
SPOT_ID
Data table ID JGI_Gene_ID Broad_Gene_ID Broad_Transcript_ID INTERPRO_1 INTERPRO_2 INTERPRO_3 GO_1 GO_2 SPOT_ID BDET_00004
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00004
BDET_00005
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00005
BDET_00006
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00006
BDET_00007
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00007
BDET_00008
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00008
BDET_00026
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00026
BDET_00033
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00033
BDET_00039
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00039
BDET_00048
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00048
BDET_00056
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00056
BDET_00069
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00069
BDET_00076
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00076
BDET_00077
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00077
BDET_00080
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00080
BDET_00092
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00092
BDET_00098
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00098
BDET_00105
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00105
BDET_00130
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00130
BDET_00131
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00131
BDET_00148
NA
NA
NA
NA
NA
NA
NA
NA
BDET_00148
8896 1845 Kbytes .Supplementary file Size Download File type/resource GPL15422_100201_BD_MS_EXP.ndf.gz
8.0 Mb
(ftp) (http) NDF
GPL15422_100201_BD_MS_EXP_HX12.ncd.gz
306 b
(ftp) (http) NCD
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