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| Status |
Public on Sep 01, 2009 |
| Title |
Tavazoie Vora Escherichia coli Affy tiling 2009 |
| Technology type |
in situ oligonucleotide |
| Distribution |
custom-commercial |
| Organism |
Escherichia coli |
| Manufacturer |
Affymetrix |
| Manufacture protocol |
We designed an Affymetrix tiling array for the MG1655 E. coli genome, containing probes that cover the entire genome at a resolution of 4 bp between steps; however, the steps alternate strand coverage, so there is an 8 bp step between probes on the same strand. There are a total of 2.47 million probes on the array, of which 2,300,160 directly enter analysis as E. coli probe pairs. The Affymetrix system pairs each 25-mer perfect match genomic sequence with a corresponding 25-mer that has a mismatch in the 13th position. The mismatch probe is intended as a cross-hybridization control. In addition to the E. coli sequences, 33,996 probe pairs are sequence-specific controls against other genomes, including B. subtilis, lambda phage, and A. thaliana. The tiling array (Ecoli_Tab520346F) is a standard-sized 200 μL-volume microarray with 5 micron features.
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| Description |
The oligonucleotides were based on NC_000913.2.
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| Contributor(s) |
Vora T, Hottes AK, Tavazoie S |
| Submission date |
May 22, 2009 |
| Last update date |
Apr 13, 2011 |
| Contact name |
yirchung Liu |
| E-mail(s) |
yliu@princeton.edu
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| Organization name |
Princeton University
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| Department |
Molecular Biology
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| Lab |
Tavazoie
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| Street address |
220 Carl Icahn Laboratory
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| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08544 |
| Country |
USA |
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| Samples (29)
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GSM412592, GSM412593, GSM412594, GSM412595, GSM412596, GSM412597
GSM412598, GSM412599, GSM412600, GSM412601, GSM412602, GSM412603, GSM412604, GSM2056048, GSM2056049, GSM2056050, GSM2056051, GSM2056052, GSM2056053, GSM2056054, GSM2056055, GSM2056056, GSM2056057, GSM2056058, GSM2056059, GSM2056060, GSM2056061, GSM2056062, GSM2056063
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| Series (3) |
| GSE16414 |
Escherichia coli Tiling Array for In vivo Protein Occupancy Display |
| GSE77686 |
E. coli transcriptome in stationary and mid-exponential phase |
| GSE77687 |
Psoralen binding across the Escherichia coli chromosome |
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| Supplementary file |
Size |
Download |
File type/resource |
| GPL8585_Ecoli_TAb520346F.bpmap.gz |
18.1 Mb |
(ftp)(http) |
BPMAP |
| GPL8585_table.txt.gz |
35.9 Mb |
(ftp)(http) |
TXT |
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