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Platform GPL5862 Query DataSets for GPL5862
Status Public on Dec 13, 2007
Title JCVI PFGRC Mycobacterium smegmatis 25K v4 array designed primarily based on strain MC2 155
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Mycolicibacterium smegmatis
Manufacturer JCVI PFGRC
Manufacture protocol 4QMS, with arrayer GENETIX, machine cycles 0, pen id 0, pen cycles 0, operator 0, humidity control 0, humidity set point0.000
Support glass
Coating aminosilane
 
Description This set includes 7148 oligonucleotides, has 25392 spots distributed in 48 blocks.
 
Web link http://pfgrc.jcvi.org/descriptionPages.shtml
Submission date Sep 13, 2007
Last update date Jul 13, 2011
Contact name PFGRC JCVI
E-mail(s) jli@jcvi.org
Phone 3017957840
Organization name J. Craig Venter Institute
Department PFGRC
Street address 9704 Medical Center Drive
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Samples (27) GSM436644, GSM436645, GSM436646, GSM436647, GSM436648, GSM436649 
Series (3)
GSE17520 M. smegmatis response to energy- and oxygen-limitation in continuous culture
GSE19145 Transciptional profile of a M. smegmatis mc2155 ΔsigF strain under standard growth conditions
GSE56083 Determining the M. smegmatis DosR regulon
Relations
Alternative to GPL13909

Data table header descriptions
ID
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 MC2 155 Target map of strain MC2 155
ORF primary target linkin Entrez Gene
SPOT_ID

Data table
ID SEQUENCE GC% Internal Repeat Score Self-Annealing Score Primary Strain Primary Target Common Name of Primary Target Gene Symbol Strain MC2 155 ORF SPOT_ID
4QMS00001_A_1 TTTGTGGTGTTGGCTGTTGTGGCGGCTGTGGCGGTGATCGTCTGGCGATCACGACACGGCCAAGAGGTTT 58.57 32 125 MC2 155 MSMEG_0009 hypothetical protein MSMEG_0009::70::100.0::4.4E-11::+ MSMEG_0009
4QMS00001_A_10 CGGCCGCGAAGGTGGCATGGCCACCCGCGAGGTGACTCCTGAGCTCGTCGAATCCGACGACGAGGACTGA 67.14 31 92 MC2 155 MSMEG_3443 hypothetical protein MSMEG_3443::70::100.0::2.6E-11::+ MSMEG_3443
4QMS00001_A_11 GTCGGACAGCACACCGCCGTCGCGTTTGGTTCGGATGATGGTTGGCGCGTCGATACCCGGATCCTACTGA 61.43 30 67 MC2 155 MSMEG_1674 hypothetical protein MSMEG_1674::70::100.0::4.2E-11::+ MSMEG_1674
4QMS00001_A_12 ACGAACGTGACACGGCTTCGCCAGAAGACGAGAACGAGCACGATCGCTGGCTGCGTCAGAACGTTCCGCC 61.43 31 115 MC2 155 MSMEG_5484 conserved hypothetical protein MSMEG_5484::70::100.0::2.6E-11::+ MSMEG_5484
4QMS00001_A_13 GGTCGTCGGCGTCATCCTGCTGGTCGTTGGCCTGCTCATGATGCTGATGGGGCGGACGGGTCACGCCATC 65.71 33 100 MC2 155 MSMEG_3327 hypothetical protein MSMEG_3327::70::100.0::4.2E-11::+ MSMEG_3327
4QMS00001_A_14 CATGCTAGGGCCCGCGATGAGTTTCGCCGCGCATTGCCGTCTGCATTGGTACGTGATCGCACCGATTCGA 60.0 31 81 Obsolete Obsolete Obsolete --Obsolete
4QMS00001_A_15 ATACGTGAGCTCGCAGCCTCGCGAGAGGTGCTCGACGGGGTCATCGCGAACGCGTCTGTGCCGATTCCCA 64.29 29 86 MC2 155 MSMEG_3413 MerR-family transcriptional regulator; this gene contains a frame shift which is not the result of sequencing error; identified by match to protein family HMM PF00376 MSMEG_3413::70::100.0::1.1E-11::+ MSMEG_3413
4QMS00001_A_16 ACTGGCCACGGCCGCTAACGGTAGCCTGACCAGCTATGCCGCGATCATTCGACATGGCCACCGAGTACGA 61.43 30 111 Obsolete Obsolete Obsolete --Obsolete
4QMS00001_A_17 ACGCAACTCCTCCTGCTCGGGGGTGTATCCGATCCGCATCCGCTGCATCCTCACTGCTCAAGCGACCTGA 61.43 30 75 MC2 155 MSMEG_5905 hypothetical protein MSMEG_5905::70::100.0::4.2E-11::+ MSMEG_5905
4QMS00001_A_18 CCGATCCGGTCCGCCTGATTCCGACGACGCGCATGCGCATTCCTTCCTAAACCGGGTGAAAACCCTCTAA 58.57 31 85 MC2 155 MSMEG_2479 hypothetical protein MSMEG_2479::70::100.0::2.5E-11::+ MSMEG_2479
4QMS00001_A_19 TGAACCGCGTGAATGAGGACTGGCTCGCCGTGATCGTCGGTCTCGCACTGCTGGGACTGATCCTGGCCGG 64.29 33 78 MC2 155 MSMEG_0440 hypothetical protein MSMEG_0440::70::100.0::4.1E-11::+ MSMEG_0440
4QMS00001_A_2 AAGGCGCGGCGCAAGGGTCAGGCCGAGTCGGCGCCGTTCGCCTCCGCGAGCCGCTCATGCAGCCGCGCGC 77.14 32 152 Obsolete Obsolete Obsolete --Obsolete
4QMS00001_A_20 AGTGCATCGACACGAACCGGCACTGACCTTCGCGGCGCACCGCTCTCGAACACATCAAGCACGGACAGTT 60.0 31 94 Obsolete Obsolete Obsolete MSMEG_3342::70::100.0::1.6E-11::- --Obsolete
4QMS00001_A_21 AAGCAAGTTGCGCCGCGTCGTGTACATCGACTCTCTTCTCAGCCCGCACTGGCACCGGCTCTGGTGCTGA 61.43 31 86 Obsolete Obsolete Obsolete --Obsolete
4QMS00001_A_22 CCGTGGTCGGTTCGATGCGACGCGCGCGCTCGGATCGACAGGCGAGCTCACCCTGCTCGTGCGGCGGCTG 72.86 35 118 MC2 155 MSMEG_4015 hypothetical protein MSMEG_4015::70::100.0::2.5E-11::+,MSMEG_4016::70::100.0::2.6E-11::- MSMEG_4015
4QMS00001_A_23 TGCTCTTCTTCGAGATCCTGCTTGTCGCGGCCGTGCTGGTCATCACGTGGTTCGCGGTGTACGCGCTGTA 60.0 31 68 MC2 155 MSMEG_5791 conserved hypothetical protein MSMEG_5791::70::100.0::4.1E-11::+ MSMEG_5791
4QMS00001_A_24 ACGTCAGCAGGAGGCGATTATGTCGCAGCGGGGAAATCACGCTTTCTCGGTATCGATGTTGATTGACCTG 52.86 29 96 MC2 155 MSMEG_4052 hypothetical protein MSMEG_4052::70::100.0::2.5E-11::+ MSMEG_4052
4QMS00001_A_3 AATACCGTGCCGATCAGAGCGTCGCCGGTTCCGATCCGTTCGCCTTATTACCTCCGTCACAACGGCTCGA 58.57 29 92 MC2 155 MSMEG_2020 hyi family protein, authentic frameshift; this gene contains a frame shift which is not the result of sequencing error; identified by similarity to RF:NP_457306.1 MSMEG_2020::70::100.0::1.2E-11::+ MSMEG_2020
4QMS00001_A_4 TGGTGCACAACAAGGACAAGGCGGTCGGGATCGGCTCGGCCGCGGGATGAGTCCCGTGCGTGACGTGGTG 67.14 31 95 MC2 155 MSMEG_1627 hypothetical protein MSMEG_1627::70::100.0::2.6E-11::+ MSMEG_1627
4QMS00001_A_5 ATACCCTCTGAGTGGCTCGATCACACATGATGAAGGAGTCATCCATGGCGCAGGTCGTCGTGTACGACGA 54.29 30 88 Obsolete Obsolete Obsolete --Obsolete

Total number of rows: 8216

Table truncated, full table size 1544 Kbytes.




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