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Platform GPL21108 Query DataSets for GPL21108
Status Public on Apr 18, 2017
Title Custom NimbleGen 12-plex Bufo marinus, Bufo boreas, Xenopus tropicalis Oligo Expression Array
Technology type in situ oligonucleotide
Distribution custom-commercial
Organisms Xenopus tropicalis; Rhinella marina; Anaxyrus boreas
Manufacturer NimbleGen
Manufacture protocol See manufacturer's website
 
Description The custom Nimblegen microarray design included 135,200 60-bp probes (excluding control probes) targeting 31,367 transcript contigs from Bufo marinus, Bufo boreas, and model species Xenopus tropicalis, with 4 probes per probe-set. Probe-sets were defined as all probes that mapped to a single transcript. We used the 12-plex microarray platform (12 arrays per glass slide). Annotation was performed using the blat program to identify Bufo contigs with high sequence identity to X. tropicalis transcripts (Ensembl assembly v4.2). We ran blat with translated Bufo contigs and translated X. tropicalis transcripts (parameters: -q=dnax –t=dnax) in order to find orthologous sequences at the protein level, which is more conserved between divergent species. We parsed blat hits to remove short hits (<100 bp aligned to query) and low scoring hits (Expectation value >1.0e-12). We used the Ensembl Gene Identifier (e.g. ENSXETG00000XXXXXX) for the blat hit with longest alignment to the query as the final annotation call. We then imported annotation metadata with the biomart.org pipeline: Ensembl gene name and description, Gene Ontology (GO) terms, Ensembl protein families, Interpro protein domains. Next, we used the blast2go pipeline to annotate Bufo contigs without GO term metadata (6328 contigs). We used the blastx method with the NCBI nonredundant protein database to identify blast hits, and proceeded with blast2go pipeline with default settings.
 
Submission date Nov 08, 2015
Last update date Apr 18, 2017
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 (71) GSM1933256, GSM1933257, GSM1933258, GSM1933259, GSM1933260, GSM1933261 
Series (1)
GSE74788 Comparative study of host response to chytridiomycosis in susceptible and resistant toad species

Data table header descriptions
ID Unique probeset ID, same as SEQ_ID as used in the .ndf and .ngd files
SPOT_ID Transcriptome assembly used to design probeset. Bufo marinus and Bufo boreas transcriptome assemblies developed from RNAseq 454 sequencing run. We obtained 8520 contigs for B. marinus and 6095 contigs for B. boreas. For the microarray design, we designed probes for contigs in three categories: B. marinus-specific contigs, B. boreas-specific contigs, and X. tropicalis transcripts (19,312 transcripts). We used this design strategy to maximize the diversity of contigs on the microarray and leverage the entire available probe area. The X. tropicalis transcripts were downloaded from Ensembl database (Xtrop v4.2), and processed to reduce paralogous transcripts by clustering with CD-HIT (parameters: cd-hit-est -T 8 -c .95 -s .95 -n 8 -d 200 -r 1 -g 1).
Anno_Xtrop_Ensembl_GeneID Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Gene Identifier
Anno_Xtrop_Ensembl_Description Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Gene description
Anno_Xtrop_Ensembl_ProteinFamily_ID Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) PFAM protein family Identifier
Anno_Xtrop_Ensembl_ProteinFamily_Description Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) PFAM protein family description
Anno_Xtrop_Ensembl_Interpro_ID Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Interpro Identifier
Anno_Xtrop_Ensembl_Interpro_Description Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Interpro Description
Anno_Xtrop_Ensembl_GOterm Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Gene Ontology term identifier
Anno_Xtrop_Ensembl_GO_Description Annotation information from the ENSEMBL database (Xenopus tropicalis v4.2) Gene Ontology description
Anno_Bufo_marinus_species_subset Specifies which probe-sets used in Bufo marinus-specific analyses. Off-species probe-sets with redundant annotations were removed, as determined by Xenopus Ensembl Gene Identifier. 1: included; 0: excluded.
Anno_Bufo_boreas_species_subset Specifies which probe-sets used in Bufo boreas-specific analyses. Off-species probe-sets with redundant annotations were removed, as determined by Xenopus Ensembl Gene Identifier. 1: included; 0: excluded.

Data table
ID SPOT_ID Anno_Xtrop_Ensembl_GeneID Anno_Xtrop_Ensembl_Description Anno_Xtrop_Ensembl_ProteinFamily_ID Anno_Xtrop_Ensembl_ProteinFamily_Description Anno_Xtrop_Ensembl_Interpro_ID Anno_Xtrop_Ensembl_Interpro_Description Anno_Xtrop_Ensembl_GOterm Anno_Xtrop_Ensembl_GO_Description Anno_Bufo_marinus_species_subset Anno_Bufo_boreas_species_subset
Cluster_10 ENSXETG00000032528|GL173667.1|34653|114739||ENSXETT00000065044|ENSXETP00000062340 ENSXETG00000032528 SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998] ENSFM00740001589471 SCO SPONDIN PRECURSOR IPR006207;IPR000421;IPR002172;IPR000884;IPR001007;IPR001879;IPR001846;IPR006552;IPR000742;IPR006560;IPR014853;IPR002919;IPR004094;IPR008037 "Cystine knot, C-terminal;Coagulation factor 5/8 C-terminal type domain;Low-density lipoprotein (LDL) receptor class A repeat;Thrombospondin, type 1 repeat;von Willebrand factor, type C;GPCR, family 2, extracellular hormone receptor domain;von Willebrand factor, type D domain;VWC out;Epidermal growth factor-like domain;AWS;Uncharacterised domain, cysteine-rich;Trypsin Inhibitor-like, cysteine rich domain;Proteinase inhibitor I15, antistasin-like;Proteinase inhibitor I19, pacifastin" GO:0004867;GO:0005515;GO:0030414;GO:0018024;GO:0007186;GO:0004930;GO:0007155;GO:0005634;GO:0016020 null 1 1
Cluster_100 ENSXETG00000008299|GL173695.1|105950|183058|dnah2|ENSXETT00000018198|ENSXETP00000018198 ENSXETG00000008299 "dynein, axonemal, heavy chain 2 [Source:Jamboree;Acc:XB-GENE-5967455]" ENSFM00740001589380;ENSFM00730001521131 DYNEIN HEAVY CHAIN 2 AXONEMAL AXONEMAL BETA DYNEIN HEAVY CHAIN 2 CILIARY DYNEIN HEAVY CHAIN 2;DYNEIN HEAVY CHAIN AXONEMAL AXONEMAL BETA DYNEIN HEAVY CHAIN CILIARY DYNEIN HEAVY CHAIN IPR003593;IPR013602;IPR011704;IPR004273;IPR000767 "AAA+ ATPase domain;Dynein heavy chain, domain-2;ATPase, dynein-related, AAA domain;Dynein heavy chain domain;Disease resistance protein" GO:0016887;GO:0006200;GO:0005858;GO:0001539;GO:0030286;GO:0007018;GO:0003777;GO:0017111;GO:0005524;GO:0000166 null 1 1
Cluster_1000 ENSXETG00000008247|GL172691.1|881354|902517|sphkap|ENSXETT00000018088|ENSXETP00000018088 ENSXETG00000008247 "SPHK1 interactor, AKAP domain containing [Source:Jamboree;Acc:XB-GENE-983186]" ENSFM00250000003911 A KINASE ANCHOR SPHKAP SPHK1 INTERACTOR AND AKAP DOMAIN CONTAINING SPHINGOSINE KINASE TYPE 1 INTERACTING null null null null 1 1
Cluster_10003 ENSXETG00000005720|GL173212.1|105267|129031|ikbip|ENSXETT00000012605|ENSXETP00000012605 ENSXETG00000005720 IKBKB interacting protein [Source:Jamboree;Acc:XB-GENE-1016798] ENSFM00250000008311 INHIBITOR OF NUCLEAR FACTOR KAPPA B KINASE INTERACTING I KAPPA B KINASE INTERACTING IKBKB INTERACTING IKK INTERACTING null null null null 1 1
Cluster_10004 ENSXETG00000009196|GL173200.1|124873|138597|slc30a2|ENSXETT00000020184|ENSXETP00000020184 ENSXETG00000009196 "solute carrier family 30 (zinc transporter), member 2 [Source:Jamboree;Acc:XB-GENE-494395]" ENSFM00250000001206 ZINC TRANSPORTER ZNT SOLUTE CARRIER FAMILY 30 MEMBER IPR002524 Cation efflux protein GO:0008324;GO:0006812;GO:0055085;GO:0016021 null 1 1
Cluster_10006 ENSXETG00000011102|GL172736.1|1409011|1413834|ttc32|ENSXETT00000024928|ENSXETP00000024928 ENSXETG00000011102 tetratricopeptide repeat domain 32 [Source:Jamboree;Acc:XB-GENE-1001928] ENSFM00500000276070 TETRATRICOPEPTIDE REPEAT 32 TPR REPEAT 32 IPR019734;IPR013026;IPR001440;IPR013105 Tetratricopeptide repeat;Tetratricopeptide repeat-containing domain;Tetratricopeptide TPR-1;Tetratricopeptide TPR2 GO:0005515 null 1 1
Cluster_10008 ENSXETG00000023144|GL172690.1|2499233|2516817|mfap3l|ENSXETT00000050054|ENSXETP00000050054 ENSXETG00000023144 microfibrillar-associated protein 3-like [Source:Jamboree;Acc:XB-GENE-940784] ENSFM00250000004073 ASSOCIATED 3 PRECURSOR IPR007110;IPR003599;IPR003598;IPR013098;IPR013151 Immunoglobulin-like domain;Immunoglobulin subtype;Immunoglobulin subtype 2;Immunoglobulin I-set;Immunoglobulin GO:0005515 null 1 1
Cluster_10009 BuMa-contig00212 null null null null null null null null 1 1
Cluster_1001 ENSXETG00000017841|GL173003.1|739937|794926|setd5|ENSXETT00000038702|ENSXETP00000038702 ENSXETG00000017841 SET domain containing 5 [Source:Jamboree;Acc:XB-GENE-5843081] ENSFM00250000001160 HISTONE LYSINE N METHYLTRANSFERASE 2E LYSINE N METHYLTRANSFERASE 2E EC_2.1.1.43 MYELOID/LYMPHOID OR MIXED LINEAGE LEUKEMIA 5 IPR001214 SET domain GO:0005515 null 1 0
Cluster_10010 ENSXETG00000000446|GL172924.1|1314539|1360841|papd5|ENSXETT00000000941|ENSXETP00000000941 ENSXETG00000000446 PAP associated domain containing 5 [Source:Jamboree;Acc:XB-GENE-990067] ENSFM00500000270456 NON CANONICAL POLY A RNA POLYMERASE PAPD5 EC_2.7.7.19 PAP ASSOCIATED DOMAIN CONTAINING 5 TERMINAL URIDYLYLTRANSFERASE 3 TUTASE 3 TOPOISOMERASE RELATED FUNCTION 4 2 TRF4 2 IPR002934;IPR002058 Nucleotidyl transferase domain;PAP/25A-associated GO:0016779 null 1 1
Cluster_10011 ENSXETG00000006826|GL173140.1|337976|353697|acsf2|ENSXETT00000014937|ENSXETP00000014937 ENSXETG00000006826 acyl-CoA synthetase family member 2 [Source:Jamboree;Acc:XB-GENE-993379] ENSFM00760001714805 ACYL COA SYNTHETASE FAMILY MEMBER 2 MITOCHONDRIAL PRECURSOR EC_6.2.1.- IPR020459;IPR000873 AMP-binding;AMP-dependent synthetase/ligase GO:0003824;GO:0008152 null 1 0
Cluster_10013 ENSXETG00000011164|GL172747.1|2028405|2043638|adh1c|ENSXETT00000024409|ENSXETP00000024409 ENSXETG00000011164 "alcohol dehydrogenase 1C (class I), gamma polypeptide [Source:Jamboree;Acc:XB-GENE-6041030]" ENSFM00250000000515 ALCOHOL DEHYDROGENASE EC_1.1.1.1 ALCOHOL DEHYDROGENASE IPR013154;IPR013149 "Alcohol dehydrogenase GroES-like;Alcohol dehydrogenase, C-terminal" GO:0016491;GO:0055114;GO:0046872;GO:0008270 null 1 1
Cluster_10014 ENSXETG00000012278|GL172653.1|5386191|5397866|hnf1a|ENSXETT00000026829|ENSXETP00000026829 ENSXETG00000012278 HNF1 homeobox A [Source:Jamboree;Acc:XB-GENE-484117] ENSFM00250000001804 HEPATOCYTE NUCLEAR FACTOR 1 ALPHA HNF 1 ALPHA HNF 1A TRANSCRIPTION FACTOR 1 TCF 1 IPR001356;IPR006899;IPR006897;IPR006898 "Homeobox domain;Hepatocyte nuclear factor 1, N-terminal;Hepatocyte nuclear factor 1, beta isoform, C-terminal;Hepatocyte nuclear factor 1, alpha isoform C-terminal" GO:0045893;GO:0043565;GO:0006355;GO:0005634;GO:0003700;GO:0003677 null 1 1
Cluster_10015 ENSXETG00000013234|GL172721.1|423252|451029|cdc14a|ENSXETT00000028975|ENSXETP00000028975 ENSXETG00000013234 CDC14 cell division cycle 14 homolog A [Source:Jamboree;Acc:XB-GENE-960625] ENSFM00250000001565 DUAL SPECIFICITY PHOSPHATASE EC_3.1.3.16 EC_3.1.3.- 48 CDC14 CELL DIVISION CYCLE 14 HOMOLOG IPR000387;IPR020422;IPR000340;IPR003595 "Protein-tyrosine/Dual specificity phosphatase;Dual specificity phosphatase, subgroup, catalytic domain;Dual specificity phosphatase, catalytic domain;Protein-tyrosine phosphatase, catalytic" GO:0016791;GO:0016311;GO:0008138;GO:0035335;GO:0006470;GO:0004725;GO:0016787 null 1 1
Cluster_10016 ENSXETG00000014875|GL172713.1|685090|694751|hnmt|ENSXETT00000032543|ENSXETP00000032543 ENSXETG00000014875 histamine N-methyltransferase [Source:Jamboree;Acc:XB-GENE-1001069] ENSFM00250000004451 HISTAMINE N METHYLTRANSFERASE HMT EC_2.1.1.8 IPR016673 Histamine N-methyltransferase GO:0046539 null 1 1
Cluster_10017 ENSXETG00000018848|GL172741.1|2249523|2269302|gad1|ENSXETT00000040862|ENSXETP00000040862 ENSXETG00000018848 "glutamate decarboxylase 1 (brain, 67kDa) [Source:Jamboree;Acc:XB-GENE-1011699]" ENSFM00250000000504 GLUTAMATE DECARBOXYLASE EC_4.1.1.15 KDA GLUTAMIC ACID DECARBOXYLASE GAD GLUTAMATE DECARBOXYLASE KDA IPR010977;IPR002129 Aromatic-L-amino-acid decarboxylase;Pyridoxal phosphate-dependent decarboxylase GO:0019752;GO:0016831;GO:0016829;GO:0030170;GO:0003824 null 1 1
Cluster_10018 ENSXETG00000020548|GL172720.1|79017|156175|nol4|ENSXETT00000044394|ENSXETP00000044394 ENSXETG00000020548 nucleolar protein 4 [Source:Jamboree;Acc:XB-GENE-6037484] ENSFM00250000002545 UNCHARACTERIZED null null GO:0005730 null 1 1
Cluster_10019 ENSXETG00000021074|GL172695.1|1933071|1970958|slc30a9|ENSXETT00000045558|ENSXETP00000045558 ENSXETG00000021074 "solute carrier family 30 (zinc transporter), member 9 [Source:Jamboree;Acc:XB-GENE-976698]" ENSFM00250000002884 ZINC TRANSPORTER 9 ZNT 9 SOLUTE CARRIER FAMILY 30 MEMBER 9 IPR002524 Cation efflux protein GO:0008324;GO:0006812;GO:0055085;GO:0016021;GO:0000166 null 1 1
Cluster_10020 ENSXETG00000021591|GL172760.1|528911|545050|mcam|ENSXETT00000046662|ENSXETP00000046661 ENSXETG00000021591 melanoma cell adhesion molecule [Source:Jamboree;Acc:XB-GENE-1002617] ENSFM00500000271112 CELL SURFACE GLYCOPROTEIN MUC18 PRECURSOR MELANOMA CELL ADHESION MOLECULE MELANOMA ASSOCIATED ANTIGEN MUC18 CD146 ANTIGEN IPR003598;IPR003599;IPR007110;IPR013162;IPR013151 "Immunoglobulin subtype 2;Immunoglobulin subtype;Immunoglobulin-like domain;CD80-like, immunoglobulin C2-set;Immunoglobulin" GO:0005515;GO:0016020 null 1 0
Cluster_10022 ENSXETG00000023098|GL173589.1|86270|131886|sardh|ENSXETT00000063377|ENSXETP00000062875 ENSXETG00000023098 sarcosine dehydrogenase [Source:Jamboree;Acc:XB-GENE-6038613] ENSFM00250000000791 DEHYDROGENASE MITOCHONDRIAL PRECURSOR IPR006076;IPR006222;IPR013977 "FAD dependent oxidoreductase;Glycine cleavage T-protein, N-terminal;Glycine cleavage T-protein, C-terminal barrel" GO:0006546;GO:0004047;GO:0016491;GO:0055114;GO:0005737 null 1 0

Total number of rows: 31367

Table truncated, full table size 11862 Kbytes.




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Supplementary file Size Download File type/resource
GPL21108_120524_Bufo_MS_exp.ndf.gz 8.2 Mb (ftp)(http) NDF
GPL21108_120524_Bufo_MS_exp.ngd.gz 745.9 Kb (ftp)(http) NGD
GPL21108_120524_Bufo_MS_exp_HX12.ncd.gz 312 b (ftp)(http) NCD

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