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Platform GPL3154 Query DataSets for GPL3154
Status Public on Nov 23, 2005
Title [E_coli_2] Affymetrix E. coli Genome 2.0 Array
Technology type in situ oligonucleotide
Distribution commercial
Organism Escherichia coli
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

The GeneChip® E. coli Genome 2.0 Array contains probe sets to detect transcripts from the K12 strain of E. coli and three pathogenic strains of E. coli. Using the new E. coli Genome 2.0 Array, researchers can gain a comprehensive view of three pathogenic forms of E. coli while continuing ongoing research projects with the K12 strain.

The GeneChip E. coli Genome 2.0 Array includes approximately 10,000 probe sets for all 20,366 genes present in four strains of E. coli. Due to the high degree of similarity between the E. coli strains, whenever possible, a single probe set is tiled to represent the equivalent ortholog in all four strains. The GeneChip E. coli Genome 2.0 Array tiles probe sets over the entire open reading frame (ORF) of E. coli, includes over 700 intergenic regions, probes for various antibiotic resistance markers, and incorporates additional control and reporter genes from the previous generation E. coli array.
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=ecoli-20
http://www.affymetrix.com/analysis/index.affx
Submission date Nov 23, 2005
Last update date Mar 08, 2019
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 (1564) GSM85143, GSM85144, GSM85145, GSM85146, GSM85147, GSM85148 
Series (182)
GSE3665 Global transcriptional machinery engineering in E. coli in the presence and absence of ethanol
GSE4724 Transcriptome analysis of the arginine regulon in E.coli
GSE5552 E coli O157:H7 w/t LB-Glu 7 hr biofilm cells with various chemicals

Data table header descriptions
ID Affymetrix Probe Set ID
ORF Entrez Gene Locus
GB_ACC GenBank Accession Number
SPOT_ID
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.
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.
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.
Gene Title Title of Gene represented by the probe set.
Gene Symbol A gene symbol, when one is available (from UniGene).
ENTREZ_GENE_ID Entrez Gene Database UID
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 GB_ACC SPOT_ID Species Scientific Name Annotation Date Sequence Type Representative Public ID Sequence Source Target Description Gene Title Gene Symbol ENTREZ_GENE_ID Gene Ontology Biological Process Gene Ontology Cellular Component Gene Ontology Molecular Function
1759068_at c4728 Escherichia coli Mar 11, 2009 Exemplar sequence CFT073_c4728 Affymetrix Proprietary Database CFT073_c4728 /DB_XREF=26250547 /SEG=NC_004431:-4495623,4497122 /LEN=1499 /DEF=Hypothetical protein hypothetical protein c4728 1038919
1759069_at b4351 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_mrr_b4351 Affymetrix Proprietary Database MG1655_mrr_b4351 /DB_XREF=PID:g1790811 /SEG=NC_000913:+4584519,4585433 /LEN=914 /DEF=restriction of methylated adenine methylated adenine and cytosine restriction protein mrr 948898 0009307 // DNA restriction-modification system // inferred from electronic annotation /// 9307 // DNA restriction-modification system // inferred from electronic annotation 0003677 // DNA binding // inferred from electronic annotation /// 0004519 // endonuclease activity // inferred from electronic annotation /// 3677 // DNA binding // inferred from electronic annotation /// 4519 // endonuclease activity // inferred from electronic annotation
1759070_s_at IG_1349064_1349430-r Escherichia coli Mar 11, 2009 Exemplar sequence IG_1349064_1349430-r Affymetrix Proprietary Database IG_1349064_1349430-r /SEG=NC_000913:-1349064,1349430 /LEN=366 /DEF=intergenic region
1759071_s_at b2503 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_b2503 Affymetrix Proprietary Database MG1655_b2503 /DB_XREF=PID:g1788849 /SEG=NC_000913:-2624715,2626958 /LEN=2243 /DEF=putative cytochrome C-type biogenesis protein putative cytochrome C-type biogenesis protein /// hypothetical protein /// predicted inner membrane protein /// putative cytochrome C-type biogenesis protein ECs3365 /// yfgF /// yfgF /// Z3766 1038688 913938 946968 958361 0005886 // plasma membrane // inferred from electronic annotation /// 0016020 // membrane // inferred from electronic annotation /// 0016021 // integral to membrane // inferred from electronic annotation /// 16020 // membrane // inferred from electronic annotation /// 16021 // integral to membrane // inferred from electronic annotation /// 5886 // plasma membrane // inferred from electronic annotation
1759072_s_at Z0312 Escherichia coli Mar 11, 2009 Exemplar sequence EDL933_Z0312 Affymetrix Proprietary Database EDL933_Z0312 /DB_XREF=GI:12513026 /SEG=NC_002655:+303947,304321 /LEN=374 /DEF=partial O replication protein for prophage CP-933H putative replication protein O of bacteriophage /// putative replication protein /// phage replication protein O /// partial O replication protein for prophage CP-933H /// putative replication protein O of bacteriophage BP-933W /// putative replication protein O of prophage CP-933X /// putative DNA replication protein O of prophage CP-933V c1549 /// ECs1611 /// ECs2987 /// Z0312 /// Z1450 /// Z1868 /// Z3356 1035296 913278 916691 957085 957881 959093 959824 0006260 // DNA replication // inferred from electronic annotation /// 6260 // DNA replication // inferred from electronic annotation
1759073_at b1154 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_ycfK_b1154 Affymetrix Proprietary Database MG1655_ycfK_b1154 /DB_XREF=PID:g1787400 /SEG=NC_000913:+1206724,1207353 /LEN=629 /DEF=hypothetical protein e14 prophage; predicted protein ycfK 945726
1759074_at b2273 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_yfbN_b2273 Affymetrix Proprietary Database MG1655_yfbN_b2273 /DB_XREF=PID:g1788609 /SEG=NC_000913:-2385730,2386446 /LEN=716 /DEF=orf, hypothetical protein predicted protein yfbN 946748
1759075_at b3447 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_ggt_b3447 Affymetrix Proprietary Database MG1655_ggt_b3447 /DB_XREF=PID:g1789856 /SEG=NC_000913:-3582712,3584454 /LEN=1742 /DEF=gamma-glutamyltranspeptidase gamma-glutamyltranspeptidase ggt 947947 0006750 // glutathione biosynthetic process // inferred from electronic annotation /// 6750 // glutathione biosynthetic process // inferred from electronic annotation 0042597 // periplasmic space // inferred from electronic annotation /// 42597 // periplasmic space // inferred from electronic annotation 0003840 // gamma-glutamyltransferase activity // inferred from electronic annotation /// 0008415 // acyltransferase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation /// 3840 // gamma-glutamyltransferase activity // inferred from electronic annotation /// 8415 // acyltransferase activity // inferred from electronic annotation
1759076_s_at IG_320306_320831-r Escherichia coli Mar 11, 2009 Exemplar sequence IG_320306_320831-r Affymetrix Proprietary Database IG_320306_320831-r /SEG=NC_000913:-320306,320831 /LEN=525 /DEF=intergenic region
1759077_s_at Z1340 Escherichia coli Mar 11, 2009 Exemplar sequence EDL933_Z1340 Affymetrix Proprietary Database EDL933_Z1340 /DB_XREF=GI:12514178 /SEG=NC_002655:+1261770,1262183 /LEN=413 /DEF=unknown protein encoded by cryptic prophage CP-933M hypothetical protein /// hypothetical protein ECs1076 /// Z1340 912746 958985
1759078_at c2520 Escherichia coli Mar 11, 2009 Exemplar sequence CFT073_c2520 Affymetrix Proprietary Database CFT073_c2520 /DB_XREF=26248367 /SEG=NC_004431:+2358550,2360934 /LEN=2384 /DEF=Conserved hypothetical protein hypothetical protein c2520 1037786
1759079_at c0978 Escherichia coli Mar 11, 2009 Exemplar sequence CFT073_c0978 Affymetrix Proprietary Database CFT073_c0978 /DB_XREF=26246868 /SEG=NC_004431:+940864,941964 /LEN=1100 /DEF=Putative regulator of late gene expression putative regulator of late gene expression c0978 1035781
1759080_s_at Z5948 Escherichia coli Mar 11, 2009 Exemplar sequence EDL933_Z5948 Affymetrix Proprietary Database EDL933_Z5948 /DB_XREF=GI:12519368 /SEG=NC_002655:-5471136,5473568 /LEN=2432 /DEF=putative restriction modification enzyme R subunit (endonuclease) putative restriction modification enzyme R subunit /// type I restriction-modification enzyme R subunit /// putative restriction modification enzyme R subunit (endonuclease) c5425 /// ECs5308 /// Z5948 1037140 913604 959705 0006304 // DNA modification // inferred from electronic annotation /// 6304 // DNA modification // inferred from electronic annotation 0003676 // nucleic acid binding // inferred from electronic annotation /// 0003677 // DNA binding // inferred from electronic annotation /// 0003824 // catalytic activity // inferred from electronic annotation /// 0004386 // helicase activity // inferred from electronic annotation /// 0004519 // endonuclease activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 16787 // hydrolase activity // inferred from electronic annotation /// 3676 // nucleic acid binding // inferred from electronic annotation /// 3677 // DNA binding // inferred from electronic annotation /// 3824 // catalytic activity // inferred from electronic annotation /// 4386 // helicase activity // inferred from electronic annotation /// 4519 // endonuclease activity // inferred from electronic annotation /// 5524 // ATP binding // inferred from electronic annotation
1759081_s_at IG_2342190_2342884-r Escherichia coli Mar 11, 2009 Exemplar sequence IG_2342190_2342884-r Affymetrix Proprietary Database IG_2342190_2342884-r /SEG=NC_000913:-2342190,2342884 /LEN=694 /DEF=intergenic region
1759082_s_at IG_769835_770677-r Escherichia coli Mar 11, 2009 Exemplar sequence IG_769835_770677-r Affymetrix Proprietary Database IG_769835_770677-r /SEG=NC_000913:-769835,770677 /LEN=842 /DEF=intergenic region
1759083_at b0419 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_yajO_b0419 Affymetrix Proprietary Database MG1655_yajO_b0419 /DB_XREF=PID:g1786621 /SEG=NC_000913:-436385,437431 /LEN=1046 /DEF=putative NAD(P)H-dependent xylose reductase
1759084_s_at Z1968 Escherichia coli Mar 11, 2009 Exemplar sequence EDL933_treA_Z1968 Affymetrix Proprietary Database EDL933_treA_Z1968 /DB_XREF=GI:12514908 /SEG=NC_002655:-1786041,1787498 /LEN=1457 /DEF=trehalase, periplasmic trehalase /// trehalase, periplasmic /// periplasmic trehalase treA /// treA /// treA 1035431 945757 960446 0005991 // trehalose metabolic process // inferred from electronic annotation /// 0008152 // metabolic process // inferred from electronic annotation /// 5991 // trehalose metabolic process // inferred from electronic annotation /// 8152 // metabolic process // inferred from electronic annotation 0042597 // periplasmic space // inferred from electronic annotation /// 42597 // periplasmic space // inferred from electronic annotation 0003824 // catalytic activity // inferred from electronic annotation /// 0004555 // alpha,alpha-trehalase activity // inferred from electronic annotation /// 0016787 // hydrolase activity // inferred from electronic annotation /// 0016798 // hydrolase activity, acting on glycosyl bonds // inferred from electronic annotation /// 16787 // hydrolase activity // inferred from electronic annotation /// 16798 // hydrolase activity, acting on glycosyl bonds // inferred from electronic annotation /// 3824 // catalytic activity // inferred from electronic annotation /// 4555 // alpha,alpha-trehalase activity // inferred from electronic annotation
1759085_at c0780 Escherichia coli Mar 11, 2009 Exemplar sequence CFT073_kdpD_c0780 Affymetrix Proprietary Database CFT073_kdpD_c0780 /DB_XREF=26246670 /SEG=NC_004431:-762465,765152 /LEN=2687 /DEF=Sensor protein kdpD sensor protein KdpD kdpD 1035720 0000160 // two-component signal transduction system (phosphorelay) // inferred from electronic annotation /// 0006950 // response to stress // inferred from electronic annotation /// 0007165 // signal transduction // inferred from electronic annotation /// 0016310 // phosphorylation // inferred from electronic annotation /// 0018106 // peptidyl-histidine phosphorylation // inferred from electronic annotation /// 160 // two-component signal transduction system (phosphorelay) // inferred from electronic annotation /// 16310 // phosphorylation // inferred from electronic annotation /// 18106 // peptidyl-histidine phosphorylation // inferred from electronic annotation /// 6950 // response to stress // inferred from electronic annotation /// 7165 // signal transduction // inferred from electronic annotation 0016020 // membrane // inferred from electronic annotation /// 16020 // membrane // inferred from electronic annotation 0000155 // two-component sensor activity // inferred from electronic annotation /// 0004673 // protein histidine kinase activity // inferred from electronic annotation /// 0004871 // signal transducer activity // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0016301 // kinase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016772 // transferase activity, transferring phosphorus-containing groups // inferred from electronic annotation /// 155 // two-component sensor activity // inferred from electronic annotation /// 16301 // kinase activity // inferred from electronic annotation /// 16740 // transferase activity // inferred from electronic annotation /// 16772 // transferase activity, transferring phosphorus-containing groups // inferred from electronic annotation /// 4673 // protein histidine kinase activity // inferred from electronic annotation /// 4871 // signal transducer activity // inferred from electronic annotation /// 5524 // ATP binding // inferred from electronic annotation
1759086_s_at b2855 Escherichia coli Mar 11, 2009 Exemplar sequence MG1655_ygeK_b2855 Affymetrix Proprietary Database MG1655_ygeK_b2855 /DB_XREF=PID:g1789219 /SEG=NC_000913:-2992482,2992928 /LEN=446 /DEF=putative 2-component transcriptional regulator hypothetical protein /// putative 2-component transcriptional regulator ECs3712 /// Z4176 916468 958324 0000160 // two-component signal transduction system (phosphorelay) // inferred from electronic annotation /// 0006350 // transcription // inferred from electronic annotation /// 0006355 // regulation of transcription, DNA-dependent // inferred from electronic annotation /// 160 // two-component signal transduction system (phosphorelay) // inferred from electronic annotation /// 6350 // transcription // inferred from electronic annotation /// 6355 // regulation of transcription, DNA-dependent // inferred from electronic annotation 0005622 // intracellular // inferred from electronic annotation /// 5622 // intracellular // inferred from electronic annotation 0000156 // two-component response regulator activity // inferred from electronic annotation /// 0003677 // DNA binding // inferred from electronic annotation /// 0003700 // transcription factor activity // inferred from electronic annotation /// 0043565 // sequence-specific DNA binding // inferred from electronic annotation /// 156 // two-component response regulator activity // inferred from electronic annotation /// 3677 // DNA binding // inferred from electronic annotation /// 3700 // transcription factor activity // inferred from electronic annotation /// 43565 // sequence-specific DNA binding // inferred from electronic annotation
1759087_s_at Z1777 Escherichia coli Mar 11, 2009 Exemplar sequence EDL933_Z1777 Affymetrix Proprietary Database EDL933_Z1777 /DB_XREF=GI:12514688 /SEG=NC_002655:+1633714,1634016 /LEN=302 /DEF=unknown protein encoded by prophage CP-933N hypothetical protein /// hypothetical protein ECs1513 /// Z1777 912435 959490

Total number of rows: 10208

Table truncated, full table size 7952 Kbytes.






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