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Platform GPL11156 Query DataSets for GPL11156
Status Public on Jan 10, 2011
Title HMS/Somero-Mytilus-105K Agilent-v1.0 salinity stress
Technology type in situ oligonucleotide
Distribution custom-commercial
Organisms Mytilus californianus; Mytilus galloprovincialis
Manufacturer Agilent Technologies, Inc.
Manufacture protocol Approximately 26,000 publicly available ESTs from M. californianus (ES7325872 - ES738966; ES408175 - ES387463;(Gracey et al., 2008)) and M. galloprovincialis (AJ623313 - AJ626468; AJ516092 - AJ516921; (Venier et al., 2003)). SSH to enrich for transcripts expressed in response to various stressors.

Sequences for each species were separately screened for vector contamination, clustered, assembled, and loaded into a PostgresQL database using the PartiGene bioinformatics pipeline (Parkinson et al., 2004), yielding a total of 12,961 and 1,688 putative gene transcripts (clusters) for M. californianus and M. galloprovincialis sequences, respectively. Clusters were annotated for identity against the UniRef 90 protein database using NCBI Blast, with an e-value cutoff of 10-8. Clusters were also annotated for gene ontology (GO), enzyme classification (ECC), and gene pathway (KEGG) using the program annot8r (Schmid and Blaxter, 2008), again with an e-value cutoff of 10-8. Long oligo (60-mer) probes were designed against the M. californianus clusters using the probe design program YODA (Nordberg, 2005) under default parameters, with a maximum of 5 probes per cluster. This yielded 43,969 total unique probes to 11,506 clusters, with a mean of 2.6 probes per cluster. To help control for the effects of interspecific sequence variation on probe performance, the above probes were compared to M. galloprovincialis clusters using BLAST. Probes designed to the M. californianus library that successfully aligned with the smaller M. galloprovincialis library had counterparts designed using the M. galloprovincialis sequence. This resulted in 556 matched pairs of probes, with a mean number of 4.6 mismatches per probe. Altogether, there were 44,524 unique probes that were duplicated or triplicated randomly to fill a 105k-feature microarray and in-situ synthesized by Agilent Technologies, Inc. (Santa Clara, CA, USA).
 
Description Agilent-019153

To accurately compare the transcriptomes of Mytilus galloprovincialis and M. trossulus, we chose to develop a common microarray format that could be used for both species. This microarray design consisted of probe sequences generated from the out-group species, M. californianus. M. trossulus and M. galloprovincialis are approximately 7.5 million years divergent from M. californianus, yet only 3.5 million years divergent from each other (Seed, 1992). Therefore, heterologous hybridization to the microarray allowed us to compare transcriptional responses of M. galloprovincialis and M. trossulus without the inherent sequence biases that would result from a microarray that was designed from sequences of either M. galloprovincialis or M. trossulus. A limited number of sequences (556) from ESTs from M. galloprovincialis that matched M. californianus ESTs were included on the microarray to test for the effects of sequence mismatches. Only probes that performed well for both M. galloprovincialis and M. trossulus were used in our analyses.

This is the same microarray platform as GPL9676 HMS/SomeroLab-Mytilus-105K array-v1.0, but the probe data are uploaded here separately due to the increased number of probes that had good hybridization in this study. This discrepancy was due to our stringent quality control that removed bad probes from the dataset and the fewer number of samples in this study (36 arrays in this study vs. 84 arrays in the previous study (Lockwood et al. 2010, Journal of Experimental Biology, 213, 3548-3558)).

The Platform data table reflects a condensed representation of the array's replicate features. The full array layout representing all of the individual features is linked as a supplementary file at the foot of this record.
 
Submission date Nov 03, 2010
Last update date Mar 24, 2011
Contact name Brent L Lockwood
E-mail(s) blockwoo@stanford.edu
Phone 831-655-6238
Organization name Hopkins Marine Station of Stanford University
Department Biology
Lab George N. Somero
Street address 120 Oceanview Blvd.
City Pacific Grove
State/province CA
ZIP/Postal code 93950
Country USA
 
Samples (36) GSM617055, GSM617056, GSM617057, GSM617058, GSM617059, GSM617060 
Series (1)
GSE25111 Transcriptomic responses to salinity stress in invasive and native blue mussels (genus Mytilus)

Data table header descriptions
ID
GB_LIST NCBI GenBank accession numbers of ESTs in the gene cluster
Gene.Symbol Gene identifier that corresponds to the probe identifier (ID_REF)
SEQUENCE Oligo sequence
Blast.Hit BLAST alignment description
EC Enzyme commission number
EC.Description Enzyme commission description
GO.Accession Gene ontology accession numbers
GO.Cellular.Component Gene ontology cellular component
GO.Biological.Process Gene ontology biological process
GO.Molecular.Function Gene ontology molecular function
KEGG.Pathways Kyoto Encyclopedia of Genes and Genomes pathway numbers
KEGG.Orthology Kyoto Encyclopedia of Genes and Genomes orthology numbers
KEGG.Description Kyoto Encyclopedia of Genes and Genomes description

Data table
ID GB_LIST Gene.Symbol SEQUENCE Blast.Hit EC EC.Description GO.Accession GO.Cellular.Component GO.Biological.Process GO.Molecular.Function KEGG.Pathways KEGG.Orthology KEGG.Description
MYC00002_1 ES387464, ES389256, ES391234, ES392121, ES393392, ES395118, ES395655, ES396583 MYC00002 AGTCTTTCATGCCACATTGAAACATTCTCTGAGAAGATTTCAGCTGATCAGGTGTTGTTA similar to CG13348-PA; n=1; Nasonia vitripennis 6.1.1.20 Phenylalanine--tRNAligase. GO:0005759|GO:0000287|GO:0006432|GO:0005524|GO:0000049|GO:0005737|GO:0016874|GO:0008033|GO:0004826|GO:0006418|GO:0000166|GO:0006412|GO:0005739|GO:0004812 mitochondrial matrix|cytoplasm|mitochondrion phenylalanyl-tRNA aminoacylation|tRNA processing|tRNA aminoacylation for protein translation|translation magnesium ion binding|ATP binding|tRNA binding|ligase activity|phenylalanine-tRNA ligase activity|nucleotide binding|aminoacyl-tRNA ligase activity 00400|00970 K01889|K01889 Phenylalanine, tyrosine and tryptophan biosynthesis|Aminoacyl-tRNA biosynthesis
MYC00002_2 ES387464, ES389256, ES391234, ES392121, ES393392, ES395118, ES395655, ES396583 MYC00002 AAAATCCTGTGTTTTCTGTATATGACAGTATCAGTCCAGTTGTGACGTTACATCAGAATT similar to CG13348-PA; n=1; Nasonia vitripennis 6.1.1.20 Phenylalanine--tRNAligase. GO:0005759|GO:0000287|GO:0006432|GO:0005524|GO:0000049|GO:0005737|GO:0016874|GO:0008033|GO:0004826|GO:0006418|GO:0000166|GO:0006412|GO:0005739|GO:0004812 mitochondrial matrix|cytoplasm|mitochondrion phenylalanyl-tRNA aminoacylation|tRNA processing|tRNA aminoacylation for protein translation|translation magnesium ion binding|ATP binding|tRNA binding|ligase activity|phenylalanine-tRNA ligase activity|nucleotide binding|aminoacyl-tRNA ligase activity 00400|00970 K01889|K01889 Phenylalanine, tyrosine and tryptophan biosynthesis|Aminoacyl-tRNA biosynthesis
MYC00002_3 ES387464, ES389256, ES391234, ES392121, ES393392, ES395118, ES395655, ES396583 MYC00002 ATAAGAACTGGACTGAATGCCTTCCTTGTATTCGGTGATGTGTATAGAAGGGATACTATT similar to CG13348-PA; n=1; Nasonia vitripennis 6.1.1.20 Phenylalanine--tRNAligase. GO:0005759|GO:0000287|GO:0006432|GO:0005524|GO:0000049|GO:0005737|GO:0016874|GO:0008033|GO:0004826|GO:0006418|GO:0000166|GO:0006412|GO:0005739|GO:0004812 mitochondrial matrix|cytoplasm|mitochondrion phenylalanyl-tRNA aminoacylation|tRNA processing|tRNA aminoacylation for protein translation|translation magnesium ion binding|ATP binding|tRNA binding|ligase activity|phenylalanine-tRNA ligase activity|nucleotide binding|aminoacyl-tRNA ligase activity 00400|00970 K01889|K01889 Phenylalanine, tyrosine and tryptophan biosynthesis|Aminoacyl-tRNA biosynthesis
MYC00002_4 ES387464, ES389256, ES391234, ES392121, ES393392, ES395118, ES395655, ES396583 MYC00002 TTCCAAGGAGAATGGTTAGAAGTGTTGGGTTGTGGCATTATGGAACAAGAACTTTTAACT similar to CG13348-PA; n=1; Nasonia vitripennis 6.1.1.20 Phenylalanine--tRNAligase. GO:0005759|GO:0000287|GO:0006432|GO:0005524|GO:0000049|GO:0005737|GO:0016874|GO:0008033|GO:0004826|GO:0006418|GO:0000166|GO:0006412|GO:0005739|GO:0004812 mitochondrial matrix|cytoplasm|mitochondrion phenylalanyl-tRNA aminoacylation|tRNA processing|tRNA aminoacylation for protein translation|translation magnesium ion binding|ATP binding|tRNA binding|ligase activity|phenylalanine-tRNA ligase activity|nucleotide binding|aminoacyl-tRNA ligase activity 00400|00970 K01889|K01889 Phenylalanine, tyrosine and tryptophan biosynthesis|Aminoacyl-tRNA biosynthesis
MYC00002_5 ES387464, ES389256, ES391234, ES392121, ES393392, ES395118, ES395655, ES396583 MYC00002 CCACAGAGAATATACAACATGTCTTTCTGGCTAACAGACGGATATAGCGAGAATGATTTT similar to CG13348-PA; n=1; Nasonia vitripennis 6.1.1.20 Phenylalanine--tRNAligase. GO:0005759|GO:0000287|GO:0006432|GO:0005524|GO:0000049|GO:0005737|GO:0016874|GO:0008033|GO:0004826|GO:0006418|GO:0000166|GO:0006412|GO:0005739|GO:0004812 mitochondrial matrix|cytoplasm|mitochondrion phenylalanyl-tRNA aminoacylation|tRNA processing|tRNA aminoacylation for protein translation|translation magnesium ion binding|ATP binding|tRNA binding|ligase activity|phenylalanine-tRNA ligase activity|nucleotide binding|aminoacyl-tRNA ligase activity 00400|00970 K01889|K01889 Phenylalanine, tyrosine and tryptophan biosynthesis|Aminoacyl-tRNA biosynthesis
MYC00004_3 ES387466 MYC00004 ATCAAATTTACAAAATCTTGACATTCAAGTTGTTCATGTTTTAGTGTATGCATCATGATG No Significant Hit
MYC00004_4 ES387466 MYC00004 GGGTTTCGAGTGAAATATTCTAATATTGCAATTCCTTCTCATATGTTGTATATTCTAAGT No Significant Hit
MYC00004_5 ES387466 MYC00004 GAAGTTTTGATTTCAGTATCACTATAATGATGATTGAGCTATTACAACCAGAAATGTATT No Significant Hit
MYC00006_1 ES387468, ES387934 MYC00006 GAGATAATGTGAACATTCAGTGATTTCGTAATTGAGTTTTAGCGTATTTGTTGAAAAGAA No Significant Hit
MYC00006_5 ES387468, ES387934 MYC00006 AAACATCTGTGGTCACTTTTGGTGCTCATCCCTCTGTAATGTGCATTTATACAATAATAT No Significant Hit
MYC00008_3 ES387470, ES387743 MYC00008 TGTTTGCTGTTTCGAGAATCGTCTTTACCATACAAGCCAAAATGGTTTATCAGTGAACTG No Significant Hit
MYC00009_1 ES387471, ES736651 MYC00009 TCTTGTTCATTAAAGTAGGGGATCAGAACATCTCTTGTCAACCAGCAGATATTTTGCACA SJCHGC06573 protein; n=1; Schistosoma japonicum
MYC00009_2 ES387471, ES736651 MYC00009 AAAGTATTATCCGTCTATATACTCTACCACAACCAGGAACTGATTAAATCAAGACGTTTT SJCHGC06573 protein; n=1; Schistosoma japonicum
MYC00009_4 ES387471, ES736651 MYC00009 AACAAGTGTTAGGTTTAACTTAAATCTCCAGACTTGCCTCTCATTGCTACGATATAAAAT SJCHGC06573 protein; n=1; Schistosoma japonicum
MYC00011_5 ES387473, ES390372, ES391632, ES396094 MYC00011 TCGTTACTCTTATCTATCTAATCTCAATGCAATACTTGACTGAATACTTTTAAAGGATTT No Significant Hit
MYC00012_1 ES387474, ES392357, ES392527, ES392841, ES738179 MYC00012 ATAATCGGAATGATAACTAAAGATGTGGTGGCGCTATCATGTCTCACAGATGAATCAAAA Hepatic lectin; n=1; Gallus gallus GO:0016020|GO:0016021|GO:0006897|GO:0004872|GO:0005529|GO:0005488|GO:0046872|GO:0005509|GO:0005737|GO:0006817|GO:0006910|GO:0009756|GO:0030169|GO:0008329|GO:0007155 membrane|integral to membrane|cytoplasm endocytosis|phosphate transport|phagocytosis, recognition|carbohydrate mediated signaling|cell adhesion binding|sugar binding|receptor activity|metal ion binding|calcium ion binding|pattern recognition receptor activity|low-density lipoprotein binding
MYC00012_2 ES387474, ES392357, ES392527, ES392841, ES738179 MYC00012 AAATTTGAAGCCACCAGGAAGGCTTTGAAGAATCTACAGACTTCCGTAGATAACAGAATA Hepatic lectin; n=1; Gallus gallus GO:0016020|GO:0016021|GO:0006897|GO:0004872|GO:0005529|GO:0005488|GO:0046872|GO:0005509|GO:0005737|GO:0006817|GO:0006910|GO:0009756|GO:0030169|GO:0008329|GO:0007155 membrane|integral to membrane|cytoplasm endocytosis|phosphate transport|phagocytosis, recognition|carbohydrate mediated signaling|cell adhesion binding|sugar binding|receptor activity|metal ion binding|calcium ion binding|pattern recognition receptor activity|low-density lipoprotein binding
MYC00012_3 ES387474, ES392357, ES392527, ES392841, ES738179 MYC00012 GACTAACTGACCTTAAAGAAGGGGAATGGCGTTGGAATTATGATCAGACATTAGCAAAAT Hepatic lectin; n=1; Gallus gallus GO:0016020|GO:0016021|GO:0006897|GO:0004872|GO:0005529|GO:0005488|GO:0046872|GO:0005509|GO:0005737|GO:0006817|GO:0006910|GO:0009756|GO:0030169|GO:0008329|GO:0007155 membrane|integral to membrane|cytoplasm endocytosis|phosphate transport|phagocytosis, recognition|carbohydrate mediated signaling|cell adhesion binding|sugar binding|receptor activity|metal ion binding|calcium ion binding|pattern recognition receptor activity|low-density lipoprotein binding
MYC00012_5 ES387474, ES392357, ES392527, ES392841, ES738179 MYC00012 GAACTGTGGATTGTTGTTTCAAAGCAGCTATACCTGGTTGGATCTTAATTGTAGTGATAA Hepatic lectin; n=1; Gallus gallus GO:0016020|GO:0016021|GO:0006897|GO:0004872|GO:0005529|GO:0005488|GO:0046872|GO:0005509|GO:0005737|GO:0006817|GO:0006910|GO:0009756|GO:0030169|GO:0008329|GO:0007155 membrane|integral to membrane|cytoplasm endocytosis|phosphate transport|phagocytosis, recognition|carbohydrate mediated signaling|cell adhesion binding|sugar binding|receptor activity|metal ion binding|calcium ion binding|pattern recognition receptor activity|low-density lipoprotein binding
MYC00013_5 ES387475, ES390970 MYC00013 ATATTCACGTTTTATTAGTTGCAAGCGTATTGTTTGCCTTTGGCCAATTGCAACAATTCT No Significant Hit

Total number of rows: 14279

Table truncated, full table size 4643 Kbytes.




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Supplementary file Size Download File type/resource
GPL11156_105K_Agilent_v1.0_full_layout.txt.gz 2.0 Mb (ftp)(http) TXT

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