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| Status |
Public on Sep 19, 2006 |
| Title |
JCVI PFGRC Streptococcus mutans 10K v2.1 array designed primarily based on strain UA159 [FULL_FEATURE_LAYOUT] |
| Technology type |
spotted oligonucleotide |
| Distribution |
non-commercial |
| Organism |
Streptococcus mutans |
| Manufacturer |
TIGR PFGRC |
| Manufacture protocol |
2QSM, with arrayer LUCIDEA, mode Normal, replicates 4, repeats 1, slide_dips 38, machine cycles 6075497, pen id 10185, pen cycles -1, operator cs, humidity control On, humidity set point65
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| Coating |
Epoxy |
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| Description |
This set includes 1948 oligonucleotides, has 10752 spots distributed in 96 blocks.
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| Web link |
http://pfgrc.tigr.org/descriptionPages.shtml
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| Submission date |
Sep 18, 2006 |
| Last update date |
Oct 18, 2013 |
| Contact name |
PFGRC JCVI |
| E-mail(s) |
[email protected]
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| Phone |
3017957840
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| Organization name |
J. Craig Venter Institute
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| Department |
PFGRC
|
| Street address |
9704 Medical Center Drive
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
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| Samples (74)
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GSM218557, GSM218558, GSM218559, GSM218560, GSM218561, GSM218562
GSM218563, GSM218564, GSM219984, GSM219985, GSM220035, GSM220036, GSM220037, GSM220038, GSM220039, GSM220040, GSM226166, GSM226171, GSM226173, GSM226174, GSM226176, GSM226177, GSM226178, GSM226180, GSM226187, GSM226188, GSM226189, GSM226190, GSM236979, GSM236980, GSM236981, GSM236982, GSM236983, GSM236984, GSM236985, GSM236986, GSM238694, GSM238695, GSM238696, GSM238697, GSM238698, GSM238699, GSM238735, GSM238737, GSM238739, GSM238743, GSM238744, GSM238745, GSM238748, GSM238755, GSM238757, GSM238758, GSM241779, GSM241786, GSM241798, GSM241799, GSM241884, GSM242730, GSM242731, GSM242733, GSM290393, GSM290395, GSM290515, GSM290517, GSM290622, GSM290624, GSM290642, GSM298016, GSM298017, GSM298018, GSM298037, GSM298038, GSM298040, GSM298042
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| Series (6)
|
| GSE8544 |
Effects of Oxygen on Virulence Traits of Streptococcus mutans |
| GSE8850 |
The Role of CcpA in Gene Regulation in Streptococcus mutans |
| GSE8922 |
Role of EIIABMan and EIIGlc in regulation of energy metabolism, biofilms, and competence in Streptococcus mutans |
| GSE9382 |
The Role of RelA of Streptococcus mutans in Global Control of Gene Expression |
| GSE9641 |
The CodY Regulon in Streptoccus mutans |
| GSE11773 |
Influence of BrpA on critical virulence attributes of Streptococcus mutans |
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| Data table header descriptions |
| ID |
Unique identification of each spot |
| Row |
Row of slide |
| Column |
Colunm of slide |
| Meta Row |
Meta row of slide |
| Meta Column |
Meta colunm of slide |
| Sub Row |
Row of block |
| Sub Column |
Colunm of block |
| Oligo ID |
Oligo identification |
| SEQUENCE |
Oligo sequence |
| GC% |
GC content of the sequence |
| Internal Repeat Score |
Internal repeat score |
| Self-Annealing Score |
Self-anneal score |
| Primary Strain |
The strain of primary target |
| Primary Target |
Locus primarily hit by the oligo |
| Common Name of Primary Target |
Common name of primary target |
| Gene Symbol |
Gene symbol |
| Strain UA159 |
Target map of strain UA159 |
| ORF |
Locus primarily hit by the oligo |
| SPOT_ID |
spot identifier |
| Data table |
| ID |
Row |
Column |
Meta Row |
Meta Column |
Sub Row |
Sub Column |
Oligo ID |
SEQUENCE |
GC% |
Internal Repeat Score |
Self-Annealing Score |
Primary Strain |
Primary Target |
Common Name of Primary Target |
Gene Symbol |
Strain UA159 |
ORF |
SPOT_ID |
| 1 |
1 |
1 |
1 |
1 |
1 |
1 |
2SM00001_C_1 |
GGTTCATCTTTTTTCCTTTGTTAAGCTTATTTATTATGATATAATGAAGTATTCAATTGAAGAAAAAGTC |
24.29 |
33 |
128 |
UA159 |
SMU.1047c |
hypothetical protein |
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SMU.1047c::70::100.0::1.0E-11::+ |
SMU.1047c |
|
| 2 |
1 |
2 |
1 |
1 |
1 |
2 |
2SM00001_G_1 |
GAAAATCGAAAAAGACTTCTCAGACAAGAGGCTTTAGGGCATTTTTTGATATAATAAGAAAAAAGATTAA |
28.57 |
31 |
87 |
UA159 |
SMU.1456c |
hypothetical protein |
|
SMU.1456c::70::100.0::8.4E-12::+ |
SMU.1456c |
|
| 3 |
1 |
3 |
1 |
1 |
1 |
3 |
2SM00001_K_1 |
TGAGGAAAATTCGTTTTTTAAAATTGTCCAAGTTCCTAAATCCAAAGGCATTGGCTTTGATATCTTTGAT |
31.43 |
31 |
99 |
UA159 |
SMU.2090c |
conserved hypothetical protein |
|
SMU.2090c::70::100.0::7.1E-12::+ |
SMU.2090c |
|
| 4 |
1 |
4 |
1 |
1 |
1 |
4 |
2SM00001_O_1 |
GCTTTTCGAAAGAAAAATCATAATGATTTGCGACACTCTGAAAGACTGCTATCAACTAACTTTCAGAGTG |
35.71 |
31 |
106 |
UA159 |
SMU.457 |
hypothetical protein |
|
SMU.457::70::100.0::6.5E-12::+ |
SMU.457 |
|
| 5 |
1 |
5 |
1 |
1 |
1 |
5 |
2SM00001_D_1 |
CAGTTACACCAAATTCTTCTTCAATCGCTTTTACAAGATCGTTAAGCTCAAGGATTGAAGCTTCTTTAAT |
34.29 |
31 |
123 |
UA159 |
SMU.959c |
hypothetical protein |
|
SMU.960::70::100.0::2.9E-12::-,SMU.959c::70::100.0::4.3E-12::+ |
SMU.959c |
|
| 6 |
1 |
6 |
1 |
1 |
1 |
6 |
2SM00001_H_1 |
GCAGGCTAAAAATGATGATGTTGAAACTTTTGATAGTTTTGATGATTGGAAATCAGAGATGAGTGCCTAT |
34.29 |
32 |
90 |
UA159 |
SMU.895 |
possible DNA-damage-inducible protein |
|
SMU.895::70::100.0::4.0E-12::+ |
SMU.895 |
|
| 7 |
1 |
7 |
1 |
1 |
1 |
7 |
2SM00001_L_1 |
ATCAAGCTGTAGGCAAACAATATACCTACGGTAAAGGTATGGAGGAACTATCTGAAGTAGAACAACTACA |
38.57 |
31 |
94 |
UA159 |
SMU.1356c |
putative transposase fragment |
|
SMU.1356c::70::100.0::3.7E-12::+ |
SMU.1356c |
|
| 8 |
1 |
8 |
1 |
2 |
1 |
1 |
2SM00001_C_1 |
GGTTCATCTTTTTTCCTTTGTTAAGCTTATTTATTATGATATAATGAAGTATTCAATTGAAGAAAAAGTC |
24.29 |
33 |
128 |
UA159 |
SMU.1047c |
hypothetical protein |
|
SMU.1047c::70::100.0::1.0E-11::+ |
SMU.1047c |
|
| 9 |
1 |
9 |
1 |
2 |
1 |
2 |
2SM00001_G_1 |
GAAAATCGAAAAAGACTTCTCAGACAAGAGGCTTTAGGGCATTTTTTGATATAATAAGAAAAAAGATTAA |
28.57 |
31 |
87 |
UA159 |
SMU.1456c |
hypothetical protein |
|
SMU.1456c::70::100.0::8.4E-12::+ |
SMU.1456c |
|
| 10 |
1 |
10 |
1 |
2 |
1 |
3 |
2SM00001_K_1 |
TGAGGAAAATTCGTTTTTTAAAATTGTCCAAGTTCCTAAATCCAAAGGCATTGGCTTTGATATCTTTGAT |
31.43 |
31 |
99 |
UA159 |
SMU.2090c |
conserved hypothetical protein |
|
SMU.2090c::70::100.0::7.1E-12::+ |
SMU.2090c |
|
| 11 |
1 |
11 |
1 |
2 |
1 |
4 |
2SM00001_O_1 |
GCTTTTCGAAAGAAAAATCATAATGATTTGCGACACTCTGAAAGACTGCTATCAACTAACTTTCAGAGTG |
35.71 |
31 |
106 |
UA159 |
SMU.457 |
hypothetical protein |
|
SMU.457::70::100.0::6.5E-12::+ |
SMU.457 |
|
| 12 |
1 |
12 |
1 |
2 |
1 |
5 |
2SM00001_D_1 |
CAGTTACACCAAATTCTTCTTCAATCGCTTTTACAAGATCGTTAAGCTCAAGGATTGAAGCTTCTTTAAT |
34.29 |
31 |
123 |
UA159 |
SMU.959c |
hypothetical protein |
|
SMU.960::70::100.0::2.9E-12::-,SMU.959c::70::100.0::4.3E-12::+ |
SMU.959c |
|
| 13 |
1 |
13 |
1 |
2 |
1 |
6 |
2SM00001_H_1 |
GCAGGCTAAAAATGATGATGTTGAAACTTTTGATAGTTTTGATGATTGGAAATCAGAGATGAGTGCCTAT |
34.29 |
32 |
90 |
UA159 |
SMU.895 |
possible DNA-damage-inducible protein |
|
SMU.895::70::100.0::4.0E-12::+ |
SMU.895 |
|
| 14 |
1 |
14 |
1 |
2 |
1 |
7 |
2SM00001_L_1 |
ATCAAGCTGTAGGCAAACAATATACCTACGGTAAAGGTATGGAGGAACTATCTGAAGTAGAACAACTACA |
38.57 |
31 |
94 |
UA159 |
SMU.1356c |
putative transposase fragment |
|
SMU.1356c::70::100.0::3.7E-12::+ |
SMU.1356c |
|
| 15 |
1 |
15 |
1 |
3 |
1 |
1 |
2SM00001_C_1 |
GGTTCATCTTTTTTCCTTTGTTAAGCTTATTTATTATGATATAATGAAGTATTCAATTGAAGAAAAAGTC |
24.29 |
33 |
128 |
UA159 |
SMU.1047c |
hypothetical protein |
|
SMU.1047c::70::100.0::1.0E-11::+ |
SMU.1047c |
|
| 16 |
1 |
16 |
1 |
3 |
1 |
2 |
2SM00001_G_1 |
GAAAATCGAAAAAGACTTCTCAGACAAGAGGCTTTAGGGCATTTTTTGATATAATAAGAAAAAAGATTAA |
28.57 |
31 |
87 |
UA159 |
SMU.1456c |
hypothetical protein |
|
SMU.1456c::70::100.0::8.4E-12::+ |
SMU.1456c |
|
| 17 |
1 |
17 |
1 |
3 |
1 |
3 |
2SM00001_K_1 |
TGAGGAAAATTCGTTTTTTAAAATTGTCCAAGTTCCTAAATCCAAAGGCATTGGCTTTGATATCTTTGAT |
31.43 |
31 |
99 |
UA159 |
SMU.2090c |
conserved hypothetical protein |
|
SMU.2090c::70::100.0::7.1E-12::+ |
SMU.2090c |
|
| 18 |
1 |
18 |
1 |
3 |
1 |
4 |
2SM00001_O_1 |
GCTTTTCGAAAGAAAAATCATAATGATTTGCGACACTCTGAAAGACTGCTATCAACTAACTTTCAGAGTG |
35.71 |
31 |
106 |
UA159 |
SMU.457 |
hypothetical protein |
|
SMU.457::70::100.0::6.5E-12::+ |
SMU.457 |
|
| 19 |
1 |
19 |
1 |
3 |
1 |
5 |
2SM00001_D_1 |
CAGTTACACCAAATTCTTCTTCAATCGCTTTTACAAGATCGTTAAGCTCAAGGATTGAAGCTTCTTTAAT |
34.29 |
31 |
123 |
UA159 |
SMU.959c |
hypothetical protein |
|
SMU.960::70::100.0::2.9E-12::-,SMU.959c::70::100.0::4.3E-12::+ |
SMU.959c |
|
| 20 |
1 |
20 |
1 |
3 |
1 |
6 |
2SM00001_H_1 |
GCAGGCTAAAAATGATGATGTTGAAACTTTTGATAGTTTTGATGATTGGAAATCAGAGATGAGTGCCTAT |
34.29 |
32 |
90 |
UA159 |
SMU.895 |
possible DNA-damage-inducible protein |
|
SMU.895::70::100.0::4.0E-12::+ |
SMU.895 |
|
Total number of rows: 10752
Table truncated, full table size 1978 Kbytes.
| Supplementary data files not provided |
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