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Platform GPL84 Query DataSets for GPL84
Status Public on Mar 11, 2002
Title [Pae_G1a] Affymetrix Pseudomonas aeruginosa Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Pseudomonas aeruginosa
Manufacturer Affymetrix
Manufacture protocol see manufacturer's web site
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

This GeneChip probe array is a powerful tool for monitoring trascriptional regulation and antimicrobial agent response of P. aeruginosa. The array represents the annotated genome of P. aeruginosa strain PA01 and includes 5,549 protein-coding sequences, 18 tRNA genes, a representative of the ribosomal RNA cluster and 117 genes present in strains other than PA01.

In addition, 199 probe sets corresponding to all intergenic regions exceeding 600 base pairs have been included. The selected probes have been screened against sequence homologies in the existing database of human genes.

Keywords = high density oligonucleotide array
July 06, 2016: annotation table updated with netaffx build 35
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=paeruginosa
http://www.affymetrix.com/analysis/index.affx
Submission date Feb 19, 2002
Last update date Jul 06, 2016
Organization Affymetrix, Inc.
E-mail(s) geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (1347) GSM45588, GSM45589, GSM45590, GSM45591, GSM63125, GSM63145 
Series (161)
GSE2430 Azithromycin-treated PAO1 vs untreated PAO1
GSE2885 PA2384 and iron starvation in P. aeruginosa
GSE3090 Microarray Analysis of Pseudomonas aeruginosa Reveals Induction of Pyocin Genes in Response to Hydrogen Peroxide

Data table header descriptions
ID Affymetrix Probe Set ID
ORF Locus tag for NC_002516.1
SPOT_ID Spot identifier
Species Scientific Name The genus and species of the organism represented by the probe set.
Annotation Date The date that the annotations for this probe array were last updated. It will generally be earlier than the date when the annotations were posted on the Affymetrix web site.
Sequence Type Indicates whether the sequence is an Exemplar, Consensus or Control sequence. An Exemplar is a single nucleotide sequence taken directly from a public database. This sequence could be an mRNA or EST. A Consensus sequence, is a nucleotide sequence assembled by Affymetrix, based on one or more sequence taken from a public database.
Sequence Source The database from which the sequence used to design this probe set was taken.
Target Description GenBank description associated with the representative public identifier. Blank for some probe sets.
Representative Public ID The accession number of a representative sequence. Note that for consensus-based probe sets, the representative sequence is only one of several sequences (sequence sub-clusters) used to build the consensus sequence and it is not directly used to derive the probe sequences. The representative sequence is chosen during array design as a sequence that is best associated with the transcribed region being interrogated by the probe set. Refer to the "Sequence Source" field to determine the database used.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID
RefSeq Transcript ID References to multiple sequences in RefSeq. The field contains the ID and Description for each entry, and there can be multiple entries per ProbeSet.
Gene Ontology Biological Process Gene Ontology Consortium Biological Process derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Cellular Component Gene Ontology Consortium Cellular Component derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".
Gene Ontology Molecular Function Gene Ontology Consortium Molecular Function derived from LocusLink. Each annotation consists of three parts: "Accession Number // Description // Evidence". The description corresponds directly to the GO ID. The evidence can be "direct", or "extended".

Data table
ID ORF SPOT_ID Species Scientific Name Annotation Date Sequence Type Sequence Source Target Description Representative Public ID Gene Title Gene Symbol ENTREZ_GENE_ID RefSeq Transcript ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
AFFX-Athal_actin_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank U37281 Arabidopsis thaliana actin-2 mRNA U37281 actin 7 ACT7 830841 NM_121018 0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007010 // cytoskeleton organization // traceable author statement /// 0009416 // response to light stimulus // inferred from expression pattern /// 0009611 // response to wounding // inferred from expression pattern /// 0009733 // response to auxin // inferred from expression pattern /// 0009845 // seed germination // inferred from mutant phenotype /// 0010053 // root epidermal cell differentiation // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0032880 // regulation of protein localization // inferred from reviewed computational analysis /// 0048364 // root development // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from mutant phenotype /// 0048767 // root hair elongation // inferred from reviewed computational analysis /// 0051301 // cell division // inferred from mutant phenotype 0005618 // cell wall // inferred from direct assay /// 0005730 // nucleolus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005829 // cytosol // inferred from direct assay /// 0005856 // cytoskeleton // inferred from sequence or structural similarity /// 0005886 // plasma membrane // inferred from direct assay /// 0009506 // plasmodesma // inferred from direct assay /// 0009570 // chloroplast stroma // inferred from direct assay /// 0009941 // chloroplast envelope // inferred from direct assay 0000166 // nucleotide binding // inferred from electronic annotation /// 0005200 // structural constituent of cytoskeleton // inferred from sequence or structural similarity /// 0005515 // protein binding // inferred from physical interaction /// 0005524 // ATP binding // inferred from electronic annotation
AFFX-Athal_GAPDH_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank M64116 Arabidopsis thaliana glyceraldehyde 3-phosphate dehydrogenase C subunit (GapC) gene M64116 glyceraldehyde-3-phosphate dehydrogenase C subunit 1 GAPC1 819567 NM_111283 0006006 // glucose metabolic process // inferred from electronic annotation /// 0006007 // glucose catabolic process // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // inferred from reviewed computational analysis /// 0006094 // gluconeogenesis // traceable author statement /// 0006096 // glycolytic process // inferred from direct assay /// 0006096 // glycolytic process // inferred from sequence or structural similarity /// 0006096 // glycolytic process // inferred from reviewed computational analysis /// 0006096 // glycolytic process // traceable author statement /// 0006098 // pentose-phosphate shunt // inferred from reviewed computational analysis /// 0006833 // water transport // inferred from reviewed computational analysis /// 0006950 // response to stress // inferred from electronic annotation /// 0006972 // hyperosmotic response // inferred from reviewed computational analysis /// 0006979 // response to oxidative stress // inferred from direct assay /// 0006979 // response to oxidative stress // inferred from expression pattern /// 0007010 // cytoskeleton organization // inferred from reviewed computational analysis /// 0007030 // Golgi organization // inferred from reviewed computational analysis /// 0009060 // aerobic respiration // inferred from reviewed computational analysis /// 0009266 // response to temperature stimulus // inferred from reviewed computational analysis /// 0009408 // response to heat // inferred from expression pattern /// 0009651 // response to salt stress // inferred from expression pattern /// 0009651 // response to salt stress // inferred from reviewed computational analysis /// 0009744 // response to sucrose // inferred from expression pattern /// 0010154 // fruit development // inferred from mutant phenotype /// 0010498 // proteasomal protein catabolic process // inferred from reviewed computational analysis /// 0034976 // response to endoplasmic reticulum stress // inferred from reviewed computational analysis /// 0042542 // response to hydrogen peroxide // inferred from direct assay /// 0046686 // response to cadmium ion // inferred from expression pattern /// 0046686 // response to cadmium ion // inferred from reviewed computational analysis /// 0048316 // seed development // inferred from mutant phenotype /// 0051775 // response to redox state // inferred from direct assay /// 0055114 // oxidation-reduction process // inferred from electronic annotation 0005634 // nucleus // inferred from direct assay /// 0005737 // cytoplasm // not recorded /// 0005739 // mitochondrion // inferred from direct assay /// 0005740 // mitochondrial envelope // inferred from direct assay /// 0005774 // vacuolar membrane // inferred from direct assay /// 0005794 // Golgi apparatus // inferred from reviewed computational analysis /// 0005829 // cytosol // inferred from direct assay /// 0005829 // cytosol // traceable author statement /// 0005886 // plasma membrane // inferred from direct assay /// 0009507 // chloroplast // inferred from direct assay /// 0016020 // membrane // inferred from direct assay /// 0048046 // apoplast // inferred from direct assay 0003677 // DNA binding // inferred from electronic annotation /// 0004365 // glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity // traceable author statement /// 0005507 // copper ion binding // inferred from direct assay /// 0008886 // glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity // inferred from direct assay /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016620 // oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor // inferred from electronic annotation /// 0050661 // NADP binding // inferred from electronic annotation /// 0051287 // NAD binding // inferred from electronic annotation
AFFX-Athal_ubq_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank U84969 Arabidopsis thaliana ubiquitin (UBQ11) gene U84969
AFFX-Bsubtilis_dapB_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank L38424 Bacillus subtilis dapB, dihydropicolinate reductase, nucleotides 1358-2101 L38424
AFFX-Bsubtilis_lys_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank X17013 Bacillus subtilis lys, diaminopimelate decarboxylase, nucleotides 362-1345 X17013
AFFX-Bsubtilis_pheB_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank M24537 Bacillus subtilis pheB, phenylalanine biosynthesis associated protein, nucleotides 2017-2460 M24537
AFFX-Bsubtilis_thrC_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank X04603 Bacillus subtilis thrC, threonine synthase, nucleotides 248-1306 X04603
AFFX-Bsubtilis_trpD_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence GenBank K01391 Bacillus subtilis trpD, TrpD protein, nucleotides 2136-3149 K01391
AFFX-YEL002C_WPB1_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database X61388 SGD:YEL002C S.cerevisiae WBP1 Oligosaccharyl transferase beta glycoprotein comples, beta subunit YEL002C Wbp1p WBP1 856716 NM_001178817 0000278 // mitotic cell cycle // inferred from direct assay /// 0006486 // protein glycosylation // inferred from electronic annotation /// 0006487 // protein N-linked glycosylation // inferred from physical interaction /// 0007049 // cell cycle // inferred from direct assay /// 0018279 // protein N-linked glycosylation via asparagine // inferred from electronic annotation 0005635 // nuclear envelope // inferred from direct assay /// 0005783 // endoplasmic reticulum // inferred from direct assay /// 0005783 // endoplasmic reticulum // inferred from electronic annotation /// 0005789 // endoplasmic reticulum membrane // inferred from electronic annotation /// 0005789 // endoplasmic reticulum membrane // inferred from mutant phenotype /// 0008250 // oligosaccharyltransferase complex // inferred from physical interaction /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation 0004579 // dolichyl-diphosphooligosaccharide-protein glycotransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016757 // transferase activity, transferring glycosyl groups // inferred from electronic annotation
AFFX-YEL018W_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database U18530 SGD:YEL018W S. cerevisiae Hypothetical ORF YEL018W Eaf5p EAF5 856696 NM_001178833 0006281 // DNA repair // inferred from direct assay /// 0006281 // DNA repair // inferred from electronic annotation /// 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0006974 // cellular response to DNA damage stimulus // inferred from electronic annotation /// 0016568 // chromatin modification // inferred from electronic annotation 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005829 // cytosol // inferred from direct assay /// 0035267 // NuA4 histone acetyltransferase complex // inferred from physical interaction
AFFX-YEL024W_RIP1_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database M23316 SGD:YEL024W S.cerevisiae RIP1 Rieske iron-sulfur protein of the mitochondrial cytochrome bc1 complex YEL024W ubiquinol--cytochrome-c reductase catalytic subunit RIP1 RIP1 856689 NM_001178839 0006122 // mitochondrial electron transport, ubiquinol to cytochrome c // inferred from direct assay /// 0009060 // aerobic respiration // inferred from mutant phenotype /// 0055114 // oxidation-reduction process // inferred from electronic annotation /// 1902600 // hydrogen ion transmembrane transport // inferred from electronic annotation 0005739 // mitochondrion // inferred from direct assay /// 0005739 // mitochondrion // inferred from electronic annotation /// 0005739 // mitochondrion // inferred from physical interaction /// 0005743 // mitochondrial inner membrane // inferred from electronic annotation /// 0005750 // mitochondrial respiratory chain complex III // inferred from direct assay /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral component of membrane // inferred from electronic annotation /// 0070469 // respiratory chain // inferred from electronic annotation 0008121 // ubiquinol-cytochrome-c reductase activity // inferred from electronic annotation /// 0016491 // oxidoreductase activity // inferred from electronic annotation /// 0016679 // oxidoreductase activity, acting on diphenols and related substances as donors // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation /// 0051537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation
AFFX-YER022W_SRB4_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database L12026 SGD:YER022W S. cerevisiae SRB4 RNA polymerase II holoenzyme/mediator subunit YER022W Srb4p SRB4 856743 NM_001178913 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0006357 // regulation of transcription from RNA polymerase II promoter // inferred from electronic annotation /// 0006367 // transcription initiation from RNA polymerase II promoter // inferred from mutant phenotype /// 0045944 // positive regulation of transcription from RNA polymerase II promoter // inferred from direct assay 0005634 // nucleus // inferred from electronic annotation /// 0016592 // mediator complex // inferred from electronic annotation /// 0070847 // core mediator complex // inferred from direct assay 0001104 // RNA polymerase II transcription cofactor activity // inferred from electronic annotation /// 0001139 // core RNA polymerase II recruiting transcription factor activity // inferred from mutant phenotype /// 0001139 // core RNA polymerase II recruiting transcription factor activity // inferred from physical interaction /// 0005198 // structural molecule activity // inferred from mutant phenotype /// 0033613 // activating transcription factor binding // inferred from direct assay
AFFX-YER148W_SPT15_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database X16860 SGD:YER148W S. cerevisiae SPT15 TFIID subunit YER148W Spt15p SPT15 856891 NM_001179038 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006352 // DNA-templated transcription, initiation // inferred from electronic annotation /// 0042790 // transcription of nuclear large rRNA transcript from RNA polymerase I promoter // inferred from mutant phenotype /// 0051123 // RNA polymerase II transcriptional preinitiation complex assembly // inferred from mutant phenotype /// 0070893 // transposon integration // inferred from direct assay /// 0070898 // RNA polymerase III transcriptional preinitiation complex assembly // inferred from direct assay 0000126 // transcription factor TFIIIB complex // inferred from direct assay /// 0000500 // RNA polymerase I upstream activating factor complex // inferred from direct assay /// 0005634 // nucleus // inferred from direct assay /// 0005634 // nucleus // inferred from electronic annotation /// 0005669 // transcription factor TFIID complex // inferred from direct assay /// 0070860 // RNA polymerase I core factor complex // inferred from direct assay 0000979 // RNA polymerase II core promoter sequence-specific DNA binding // inferred from direct assay /// 0001016 // RNA polymerase III regulatory region DNA binding // inferred from direct assay /// 0001026 // TFIIIB-type transcription factor activity // inferred by curator /// 0001075 // RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly // inferred by curator /// 0001102 // RNA polymerase II activating transcription factor binding // inferred from direct assay /// 0001102 // RNA polymerase II activating transcription factor binding // inferred from physical interaction /// 0001179 // RNA polymerase I transcription factor binding // inferred from direct assay /// 0001179 // RNA polymerase I transcription factor binding // inferred from physical interaction /// 0001186 // RNA polymerase I transcription factor recruiting transcription factor activity // inferred from direct assay /// 0001186 // RNA polymerase I transcription factor recruiting transcription factor activity // inferred from physical interaction /// 0003677 // DNA binding // inferred from electronic annotation /// 0003682 // chromatin binding // inferred from direct assay /// 0008301 // DNA binding, bending // inferred from direct assay /// 0043565 // sequence-specific DNA binding // inferred from direct assay
AFFX-YFL039C_ACT1_at --control Pseudomonas aeruginosa Oct 6, 2014 Control sequence Saccharomyces Genome Database V01288 SGD:YFL039C S. cerevisiae ACT1 Actin YFL039C actin ACT1 850504 NM_001179927 0000001 // mitochondrion inheritance // traceable author statement /// 0000011 // vacuole inheritance // inferred from genetic interaction /// 0000011 // vacuole inheritance // inferred from mutant phenotype /// 0000132 // establishment of mitotic spindle orientation // traceable author statement /// 0000910 // cytokinesis // inferred from direct assay /// 0000916 // actomyosin contractile ring contraction // inferred from direct assay /// 0000916 // actomyosin contractile ring contraction // inferred from mutant phenotype /// 0001300 // chronological cell aging // inferred from mutant phenotype /// 0006281 // DNA repair // inferred from direct assay /// 0006357 // regulation of transcription from RNA polymerase II promoter // inferred from direct assay /// 0006887 // exocytosis // traceable author statement /// 0006897 // endocytosis // inferred from mutant phenotype /// 0007119 // budding cell isotropic bud growth // traceable author statement /// 0009306 // protein secretion // inferred from genetic interaction /// 0009306 // protein secretion // inferred from mutant phenotype /// 0016573 // histone acetylation // inferred from direct assay /// 0030010 // establishment of cell polarity // inferred from genetic interaction /// 0030037 // actin filament reorganization involved in cell cycle // traceable author statement /// 0030050 // vesicle transport along actin filament // traceable author statement /// 0030476 // ascospore wall assembly // inferred from direct assay /// 0031505 // fungal-type cell wall organization // traceable author statement /// 0034599 // cellular response to oxidative stress // inferred from genetic interaction 0000123 // histone acetyltransferase complex // inferred from direct assay /// 0000142 // cellular bud neck contractile ring // inferred from direct assay /// 0000812 // Swr1 complex // inferred from direct assay /// 0005737 // cytoplasm // inferred from electronic annotation /// 0005856 // cytoskeleton // inferred from electronic annotation /// 0005884 // actin filament // inferred from direct assay /// 0030479 // actin cortical patch // inferred from direct assay /// 0031011 // Ino80 complex // inferred from physical interaction /// 0032432 // actin filament bundle // inferred from direct assay /// 0035267 // NuA4 histone acetyltransferase complex // inferred from direct assay /// 0035267 // NuA4 histone acetyltransferase complex // inferred from physical interaction 0000166 // nucleotide binding // inferred from electronic annotation /// 0004402 // histone acetyltransferase activity // inferred from direct assay /// 0005200 // structural constituent of cytoskeleton // inferred from direct assay /// 0005524 // ATP binding // inferred from electronic annotation
ig_1046911_1047549_at Intergenic region between PA0981 and PA0982, 1046911-1047549, (+) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA0981 and PA0982, 1046911-1047549, (+) strand 1036911 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0044780 // bacterial-type flagellum assembly // inferred from electronic annotation /// 0045893 // positive regulation of transcription, DNA-templated // inferred from electronic annotation /// 1902208 // regulation of bacterial-type flagellum assembly // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation
ig_1047549_1046911_at Intergenic region between PA0981 and PA0982, 1046911-1047549, (-) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA0981 and PA0982, 1046911-1047549, (-) strand 1036911 0006351 // transcription, DNA-templated // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-templated // inferred from electronic annotation /// 0044780 // bacterial-type flagellum assembly // inferred from electronic annotation /// 0045893 // positive regulation of transcription, DNA-templated // inferred from electronic annotation /// 1902208 // regulation of bacterial-type flagellum assembly // inferred from electronic annotation 0005737 // cytoplasm // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation
ig_1063544_1064555_at Intergenic region between PA1003 and PA1004, 1063544-1064555, (+) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA1003 and PA1004, 1063544-1064555, (+) strand 1053544
ig_1064555_1063544_at Intergenic region between PA1003 and PA1004, 1063544-1064555, (-) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA1003 and PA1004, 1063544-1064555, (-) strand 1053544
ig_1087095_1087843_at Intergenic region between PA1030 and PA1031, 1087095-1087843, (+) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA1030 and PA1031, 1087095-1087843, (+) strand 1077095
ig_1087843_1087095_at Intergenic region between PA1030 and PA1031, 1087095-1087843, (-) strand Pseudomonas aeruginosa Oct 6, 2014 Exemplar sequence GenBank Intergenic region between PA1030 and PA1031, 1087095-1087843, (-) strand 1077095

Total number of rows: 5900

Table truncated, full table size 2930 Kbytes.






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