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Platform GPL15818 Query DataSets for GPL15818
Status Public on Sep 01, 2013
Title USACH_E_coli_9K_v1.0
Technology type spotted oligonucleotide
Distribution custom-commercial
Organism Escherichia coli
Manufacturer Microarrays Inc
Manufacture protocol Escherichia coli - Our E. coli probe set for microarrays contains 9308 long oligos to investigate four strains of Escherichia coli and three E. coli-associated plasmids. Within the probe set there are:
4,269 ORF probes from K12,
5,306 ORF probes from O157:H7 (EDL933),
5,251 ORF probes from O157:H7 (Sakai)
5,366 ORF probes in CFT073
Among these gene expression probes for the E. coli-associated plasmids, 3 plasmid genes in OSAK1, 10 genes in pO157_Sakai and 97 genes in pO157_EDL933 are present in the probe set.
 
 
Submission date Jul 18, 2012
Last update date Jun 30, 2014
Contact name David Enrique Loyola
E-mail(s) dloyolac@gmail.com
Phone +56-9-74305392
Organization name OMICS Solutions, Centro Nacional de Genómica y Bioinformática
Street address Avenida Libertador Bernardo O'Higgins 340
City Santiago
State/province Santiago
ZIP/Postal code 8331150
Country Chile
 
Samples (17) GSM977853, GSM977854, GSM977855, GSM977856, GSM977857, GSM977858 
Series (3)
GSE39696 Tellurite-mediated cefotaxime (CTX) potentiation
GSE58176 Transcriptional profiling of E. coli cultures exposed to tellurite 0.5 µg/ml
GSE58912 Transcriptional profiling of E. coli cultures exposed to green or red CdTe Quantum Dots 50 µg/ml

Data table header descriptions
ID
Plate plate
Block Block
Column Column
Row Row
oligo_id oligonucleotide identificator
SEQUENCE oligonucleotide sequence
locus_k12 Locus E. coli K-12
symbol Gene Name
description
ORF_LIST
PI_LIST
GI_LIST
UniProtKB/SwissProt
SPOT_ID

Data table
ID Plate Block Column Row oligo_id SEQUENCE locus_k12 symbol description ORF_LIST PI_LIST GI_LIST UniProtKB/SwissProt SPOT_ID
1 30: D-01 1 1 1 Dye Marker Dye Marker
2 1: D-01 1 2 1 E100000297 CCCTCGCGGTGCGTGAGTGGATTGCACAGGTTAATACTGAGAAAAACATTCTCAGTTTGCTTCTGCATCC b0305 ykgD predicted DNAbinding transcriptional regulator b0305 16128290 945616 P77379
3 1: D-09 1 3 1 E100000301 ACGGAACGGGGTTAAGTCAGGTTGTCCTAAACGCTATTTTCAACCTCGTATGCCTTCTTCAGGTTTATGT E100000301
4 1: D-17 1 4 1 E100000305 CCAAATTGGGGATGCAGTCGATCCGGCGCAGACAACTGATCGACGCCACACTGGAAGCAATAAATGAAGT b0313 betI transcriptional regulator BetI b0313 49176011 944981 P17446
5 1: H-01 1 5 1 E100000321 GCTGAATTGATGACCAAAGCGGAATTTGAAAAAGTTGAATCGCAGTATGAAAAAATAGGTGATATTTCAA b0329 yahO hypothetical protein b0329 16128314 944985 P75694
6 1: H-09 1 6 1 E100000325 GCTGGGCGGCGCACATTATCGAACAACGTCAGGACAACAAAATTATCCGTCCTTCCGCCAATTATGTTGG b0333 prpC 2methylcitrate synthase b0333 16128318 947528 P31660
7 1: H-17 1 7 1 E100000329 ACGGCATTCAGCATGTGCGTACCCATGTCGATGTTTCGGATGCAACGCTAACTGCGCTGAAAGCAATGCT b0337 codA cytosine deaminase b0337 16128322 944996 P25524
8 1: L-01 1 8 1 E100000345 GATGGATAAGCTGCGTCCAGTAACCATGTCGCTACTGATTTATAGCGGCATGTTAGCTTCGCTGCTGGCG b0353 mhpT predicted 3hydroxyphenylpropionic transporter b0353 90111117 944997 P77589
9 1: L-09 1 9 1 E100000349 GATGATGAGGTGCGAAATGCCCAGTACTCCGGAAGAGAAGAAAAAGGTCCTTACTCGAGTTCGTCGTATT E100000349
10 1: L-17 1 10 1 E100000353 CAAAGAACCTTGCAGAGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTC b2860| b1996| b1402| b4273| b0361| b4579| b3045| b1578 insD4| insD3| insD2| insD6| insD1| yaiX| insD5| insD7 IS2 insertion element transposase InsAB' | CP444 prophage; IS2 insertion element transposase InsAB' | IS2 insertion element transposase InsAB' | KpLE2 phagelike element; IS2 insertion element transposase InsAB' | IS2 insertion element transposase In b2860| b1996| b1402| b4273| b0361| b4579| b3045| b1578 16128346| 16129363| 16129536| 16129937| 16130763| 16130941| 16132094| 945203| 945952| 946118| 946403| 947346| 947517| 948779| P19777| P19777| P19777| P19777| P19777| | P19777| P76167
11 1: P-01 1 11 1 E100000369 CCGCGCGTTTCTGGTCGTTGGATTTCCTGATTTTTTACGCTTACTACATTGTTTGCGTAGGACTTTTTGC b0377 sbmA predicted transporter b0377 16128362 946884 P0AFY6
12 1: P-09 1 12 1 E100000373 CGAAGATGGTTCCTTGCAGGGAATGCTGCGGGTCGCCAATTTACCGTTTGTAGGTTCTGATGTTCTGGCT b0381 ddl Dalanylalanine synthetase b0381 16128366 945313 P0A6J8
13 1: P-17 1 13 1 E100000377 GCAGATAGCGAGCAGGGCCGTCGATCCGCTTAGCCGGGAAATTTACAACTTAAAAACCGATGCAGTATTA b0385 yaiC predicted diguanylate cyclase b0385 16128370 945037 P0AAP1
14 2: D-01 1 14 1 E100000677 AAATTTTCCGATGTTACCGTCGATTTAGCCGCCCGCGTGATTCACCGGGGTGAGGAAGAGGTGCATCTCA b0694 kdpE DNAbinding response regulator in twocomponent regulatory system with KdpD b0694 16128670 945302 P21866
15 2: D-09 1 15 1 E100000681 CGATGTCAGTGATTTTTGTCATCTGCGTAGGCGTGGTGATGTGGGCAGAAGTTCAGGGTAATCCTCATCT b0698 kdpA potassiumtransporting ATPase subunit A b0698 16128674 946045 P03959
16 2: D-17 1 16 1 E100000685 AATTAGTCTCATGTCTTATGGAATGATGGTAATATGTTTTCCAACAGGCATAGTATTCTTTATTGCTCTA b0702 ybfB predicted inner membrane protein b0702 16128677 947566 P0AAU5
17 2: H-01 1 17 1 E100000701 CATCACAGCAGGTTTTAATGTTGATATTGGTGACTGGAGAGATATCTCGATTTCGACGTCATTCAATACG b0718 ybgQ predicted outer membrane protein b0718 90111165 946537 P75750
18 2: H-09 1 18 1 E100000705 TTTCTATCTTGATCCATGCCTGGATCGGCATGTGGCAGGTGTTGACCGACTACGTTAAACCGCTGGCTTT b0722 sdhD succinate dehydrogenase cytochrome b556 small membrane subunit b0722 16128697 945322 P0AC44
19 2: H-17 1 1 2 E100000709 TAACTGGCGTTCGACGTTCCAGCAGTTACCTGGTACGGGAGTCAAACCGGATCAATTCCACTCTCAAACG b0726 sucA alphaketoglutarate decarboxylase b0726 16128701 945303 P0AFG3
20 2: L-01 1 2 2 E100000725 ATGGTGGCATTTCAGAATTTCATCAAAAATTACCCTGATTCAACTTACCTGCCAAACGCCAATTATTGGC b0742 ybgF hypothetical protein b0742 16128717 947227 P45955

Total number of rows: 10944

Table truncated, full table size 1486 Kbytes.




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Supplementary file Size Download File type/resource
GPL15818_EC3001_E_coli_genelist.xls.gz 2.9 Mb (ftp)(http) XLS
GPL15818_update_06272014.txt.gz 513.2 Kb (ftp)(http) TXT

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