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Status
Public on Jul 01, 2012
Title
Agilent-020412 Yersinia pseudotuberculosis YPIII gene expression array
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Yersinia pseudotuberculosis Manufacturer
Agilent Technologies
Manufacture protocol
See manufacturer's website (http://www.agilent.com ).
Description
Sequences used for the design of the microarray (Agilent, 8 x 15K format) include three different 60-nt oligonucleotides for all 4172 chromosomal genes (ORFs > 30 codons) of the Y. pseudotuberculosis YPIII genome and six probes for the 92 genes of the virulence plasmid pYV of Y. pseudotuberculosis strain IP32953, and were obtained from the NCBI Genome GenBank (NC_010465.1 and NC_006153). The ORF-specific oligonucleotides were designed using the webdesign application eArray from Agilent (http://www.genomics.agilent.com ).
Contributor(s)
Heroven AK , Böhme K , Dersch P , Klein J , Münch R , Melzer J Submission date
Jan 06, 2012
Last update date
Jul 01, 2012
Contact name
Ann Kathrin Heroven
E-mail(s)
Annkathrin.Heroven@helmholtz-hzi.de Phone
+49-(0)53161815705
Organization name
Helmholtz Centre for Infection Research
Department
Molecular Infection Biology
Street address
Inhoffenstr. 7
City
Braunschweig
State/province
Niedersachsen
ZIP/Postal code
38124
Country
Germany
Samples (41)
GSM857311 , GSM861270 , GSM861271 , GSM861272 , GSM1035376 , GSM1035377
GSM1035378 ,
GSM1035379 ,
GSM1318658 ,
GSM1318659 ,
GSM1318660 ,
GSM1318661 ,
GSM1318662 ,
GSM1318663 ,
GSM1318664 ,
GSM1318665 ,
GSM1318666 ,
GSM1362156 ,
GSM1362157 ,
GSM1362158 ,
GSM1362159 ,
GSM1362160 ,
GSM1362161 ,
GSM1362162 ,
GSM1362163 ,
GSM2129862 ,
GSM2129863 ,
GSM2129864 ,
GSM2129865 ,
GSM2129866 ,
GSM2129867 ,
GSM2129868 ,
GSM2129869 ,
GSM2129870 ,
GSM2129871 ,
GSM2129872 ,
GSM2129873 ,
GSM2129874 ,
GSM2129875 ,
GSM2129876 ,
GSM2129877 Series (14)
GSE35043 Yersinia pseudotuberculosis ymoA mutant vs. wild type YPIII
GSE42206 Crp induces switching of the CsrB and CsrC RNAs in Yersinia pseudotuberculosis and links nutritional status to virulence
GSE54544 The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [crp mutant]
GSE54545 The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [csrA mutant]
GSE54546 The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis [rovA mutant]
GSE54547 The pyruvate-tricarboxylic acid cycle node: a focal point of virulence control in the enteric pathogen Yersinia pseudotuberculosis
GSE56475 Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray I]
GSE56476 Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection [microarray II]
GSE56477 Complex in vivo RNA-seq analysis reveal reprogramming of Yersinia from virulent to persistent mode during infection
GSE80528 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_26C-log]
GSE80529 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_26C-stat]
GSE80530 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_37C-log]
GSE80531 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis [dtatC-vs-ip_37C-stat]
GSE80532 Transcriptomic and phenotypic analysis reveals new functions for the Tat pathway in Yersinia pseudotuberculosis
Data table header descriptions ID COL Column number
ROW Row number
NAME Agilent probe ID
CONTROL_TYPE Agilent control type
GeneID NCBI Gene ID
PT_ACC GenBank protein accession
ORF Locus tag
GENOME_ACC RefSeq genome accession from which ORF identifiers are derived
GENE_SYMBOL Gene short name
GENE_NAME Gene description
ACCESSION_STRING String of GenBank protein accession-GI
CHROMOSOMAL_LOCATION String of replicon:orientation:start position-end position
SEQUENCE Probe sequence
SPOT_ID
Data table ID COL ROW NAME CONTROL_TYPE GeneID PT_ACC ORF GENOME_ACC GENE_SYMBOL GENE_NAME ACCESSION_STRING CHROMOSOMAL_LOCATION SEQUENCE SPOT_ID 1
96
164
GE_BrightCorner
pos
control
2
96
162
DarkCorner
pos
control
3
96
160
DarkCorner
pos
control
4
96
158
CUST_2083_PI390410464
FALSE
6089418 ACA70286 YPK_4024 NC_010465.1 4-alpha-L-fucosyltransferase
gb|ACA70286.1|gi|169752768
chr:-:4437937-4439022
GCAGGTAAAACAGACGAAATTTTAAGCTTTTGGCATCTTCGTATAAATCCGCACCCCAGA
5
96
156
CUST_729_PI390410464
FALSE
6087644 ACA66712 YPK_0407 NC_010465.1 Domain of unknown function DUF1813, HSP20-likeprotein
gb|ACA66712.1|gi|169749194
chr:-:447924-448286
GGACAGAGACAGTTCACCCTTATCTTGTATCCAGTCCATGCCAATATGGTGATCGTTTTC
6
96
154
CC_4_74
neg
unmapped
control
7
96
152
CUST_513_PI390410464
FALSE
6091124 ACA67454 YPK_1156 NC_010465.1 kdpD
osmosensitive K+ channel signal transductionhistidine kinase
gb|ACA67454.1|gi|169749936
chr:-:1292768-1295494
ATATACACTTTGCCTTCATTGAGGCGTTGGTGCAGATCATCGGGGGGTAAATCGACTAAA
8
96
150
CUST_5531_PI390410464
FALSE
6090097 ACA67099 YPK_0798 NC_010465.1 type VI secretion protein, VC_A0107 family
gb|ACA67099.1|gi|169749581
chr:+:906784-907284
CCCGCCAGTATGCAGGTCTAATTTGATGTTAATGCGTGCTTTAGGTATCTCATTTTGGAA
9
96
148
CUST_8001_PI390410464
FALSE
6088401 ACA68757 YPK_2480 NC_010465.1 conserved hypothetical protein
gb|ACA68757.1|gi|169751239
chr:-:2714835-2715110
GCATTCTCCAGTAATGCAGTAAGTAATTCTGTCTGACGTTTTTGCTGCTCGGCAATTTCT
10
96
146
CUST_11077_PI390410464
FALSE
6089375 ACA66475 YPK_0162 NC_010465.1 malQ
4-alpha-glucanotransferase
gb|ACA66475.1|gi|169748957
chr:+:211192-213288
CTCACCGACCTGCTCTAACATCTGCTTTAAATCACCAAAGTCACCGATACCCCAATTATG
11
96
144
SC8.3
ignore
unmapped
--ignore
12
96
142
CUST_10495_PI390410464
FALSE
6090536 ACA70149 YPK_3884 NC_010465.1 methylenetetrahydrofolate reductase
gb|ACA70149.1|gi|169752631
chr:+:4284778-4285578
GACTCAGGAAATCCAATGCATTCGTGTTGAGTGTCAGTTGGCTGATAAACTCATTAACCC
13
96
140
CUST_8978_PI390410464
FALSE
6087479 ACA69174 YPK_2900 NC_010465.1 secretion protein HlyD family protein
gb|ACA69174.1|gi|169751656
chr:+:3193618-3194604
GCTAGCGTTGCTAATAGAGCGACAATAACGGCAGCCACGATAATCTTCTTACGATTCAT
14
96
138
CUST_11165_PI390410464
FALSE
6089434 ACA69742 YPK_3475 NC_010465.1 yadE
polysaccharide deacetylase
gb|ACA69742.1|gi|169752224
chr:-:3817006-3818319
AGCTGATACAGAGAAATAGTGTCATAGCCCGCCTGTTTGAGGTAAGCCATTTGATTACTG
15
96
136
CUST_2350_PI390410464
FALSE
6088014 ACA68465 YPK_2182 NC_010465.1 ipk
4-diphosphocytidyl-2C-methyl-D-erythritolkinase
gb|ACA68465.1|gi|169750947
chr:+:2421027-2421959
ATGTTAGTCCGAGATCGGCTAATTGTTCATCAGTTAAACCACATTGCCACAGTAGGTTGA
16
96
134
CUST_11161_PI390410464
FALSE
6088258 ACA69968 YPK_3701 NC_010465.1 phnN
phosphonate metabolismprotein/1,5-bisphosphokinase (PRPP-forming) PhnN
gb|ACA69968.1|gi|169752450
chr:+:4088655-4089236
GGTCAGATAACGGTGTATCAAGGGTCAGTAATTGCTGTAATTGGTTCAGGGTGTGTTGTA
17
96
132
CUST_5875_PI390410464
FALSE
6089747 ACA67678 YPK_1384 NC_010465.1 narP
two component transcriptional regulator, LuxRfamily
gb|ACA67678.1|gi|169750160
chr:-:1526591-1527220
CAAATACATAATCGTCGCGGCAACCCGTGAGCGCACATTTAATTTACGCAATAAATTACG
18
96
130
NA
ignore
--ignore
19
96
128
CUST_3218_PI390410464
FALSE
6089283 ACA68754 YPK_2477 NC_010465.1 aroP
amino acid permease-associated region
gb|ACA68754.1|gi|169751236
chr:-:2712309-2713682
GTTCCACGGGAAAAGAGACAGAAGCACCGTCAGTGAGCCAATATAAAAAATAAGAATGCG
20
96
126
CUST_10301_PI390410464
FALSE
6087390 ACA69793 YPK_3526 NC_010465.1 mraW
S-adenosyl-methyltransferase MraW
gb|ACA69793.1|gi|169752275
chr:-:3873856-3874818
TCCAGATCCCGCACATAATGTGCTAAATCAGAAAAAGGACCATGTACGATAGAGAAACGG
15744 2942 Kbytes .Supplementary file Size Download File type/resource GPL15095_25_11_2009.gal.gz
419.5 Kb
(ftp) (http) GAL
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