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Platform GPL14026 Query DataSets for GPL14026
Status Public on Aug 12, 2011
Title Histoplasma_capsulatum_G217B_WGTA_026589
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Histoplasma capsulatum
Manufacturer CombiMatrix Corporation (Mukilteo, WA)
Manufacture protocol Arrays were designed based on the Washington University Genome Sequencing Center (GSC) Histoplasma capsulatum strain G217B genome assembly as of 11/30/2004. Degenerate sequence and transposable elements were removed from the assembly using RepeatMasker with default parameters and the repeat families determined by the GSC. The remaining sequence was tiled with 50mer probes at an average frequency of one probe every 60 base pairs. Probe spacing was adjusted to minimize variation in melting temperature, and a subset of probes were truncated to optimize synthesis, in collaboration with CombiMatrix. The number of arrays used to tile a given contig was minimized, and the location of tiling probes was randomized within a given array. In addition, each array contained a common set of control probes, viz.: quality control (QC) and negative control (NC) probes designed by CombiMatrix; positive control probes tiling the genomic loci and non-genic flanking sequence of TEF1(P40911), TYR1, and CBP1(AF006209); and probes specific to a spike-in control sequence. Arrays were synthesized by CombiMatrix.
 
 
Contributor(s) Foo CK, Sil A
Submission date Aug 02, 2011
Last update date Aug 12, 2011
Contact name Mark Voorhies
E-mail(s) mark.voorhies@ucsf.edu
Organization name University of California
Department Microbiology and Immunology
Lab Anita Sil
Street address 513 Parnassus, S472
City San Francisco
State/province CA
ZIP/Postal code 94143-0414
Country USA
 
Samples (1) GSM771275
Series (1)
GSE31155 Experimental annotation of Histoplasma capsulatum transcribed regions using high-resolution tiling arrays

Data table header descriptions
ID
COMBI_ID CombiMatrix probe ID
SPOT_ID
SEQUENCE
RANGE_GB
RANGE_START
RANGE_END
RANGE_STRAND
ROW Row position on array from CombiMatrix GAL file.
COL Column position on array from CombiMatrix GAL file.

Data table
ID COMBI_ID SPOT_ID SEQUENCE RANGE_GB RANGE_START RANGE_END RANGE_STRAND ROW COL
136357 76df025a70d0748672dcaf7c924bd1fd_76df025a70d0748672dcaf7c924bd1fd QC-3prime TGACTGACTGGACTGTGGGTGTGCGATACGTGTCC 1 1
136358 897052f32640e2baa47cc6764a38caa5_897052f32640e2baa47cc6764a38caa5 QC-5prime TGGGTGTGCGATACGTGTCCGACTGACTGACTGAC 1 2
136359 a684c01da416fc39011fdd518b94aed5 HISTO_DM.Contig933|sl-56186-56227|AS ATTGACACGGCAAAATTCGTGGCAGGGCGGGAGAGATATCTT ABBT01000057.1 56186 56227 - 1 3
136360 ed1b7ad7fa98c5b39fa5ba5fd29c76a7 HISTO_DM.Contig940|sl-269115-269156|AS CGAATGTGGCGACTCAGCAAGTTCGGAGGGCTTCTGTGGGTG ABBT01000060.1 269115 269156 - 1 4
136361 78c76e6a58a08a3eb4bdadd689381e54 HISTO_ZL.Contig1161c:170452,173949 TYR1|sl-2240-2289| GTGGAGCAAGCATTGGCGGAGTACCTTTCTGTTACCGTTACGATTACTAG ABBT01000205.1 978665 978714 + 1 5
136362 af6aefdc0fc33dd69e589c4475852d28 HISTO_DM.Contig940|sl-275365-275413|AS AATTGTTATTTATTGTTTTGTAACTATCCCAGGGGCTGTTCCTCTGGCA ABBT01000060.1 275365 275413 - 1 6
136363 b8a8a3d7107b3bb86a5e2997da3b88c5 HISTO_DM.Contig933|sl-96719-96766| CAGTCCAACAATTTCTGCTCCTGCACCTCCTCCAATACAAACGACATG ABBT01000057.1 96719 96766 + 1 7
136364 8f3b6bb89e079adb0dd0287642c11af3 HISTO_ZL.Contig1117:143635,146491 CBP1|sl-217-264|AS GAAGGCCAATTTGCTATGGCGGGGTAATTGACTTCTGATGTTGACGAT ABBT01000201.1 143851 143898 - 1 8
136365 c26c476be21cc63a7c4b7f333fe31082 HISTO_DM.Contig933|sl-144003-144050| TTGAATGGGACCCCCAATCAAAGAAATACTCGGAAGGAAACAAAGCGG ABBT01000057.1 144003 144050 + 1 9
136366 62ba39b10c1bd733a24474248108dfeb HISTO_DM.Contig933|sl-184520-184562| CAAACCTCCTACCAGCTTTCAACAGTGGCCACGCTGCTACTAT ABBT01000057.1 184520 184562 + 1 10
136367 3a13c408f91517d26f5ecb7fc9c195cd HISTO_ZL.Contig1117:143635,146491 CBP1|sl-1494-1543|AS GGGCAAGTTAGTCATGTTCAAGCCAAAATGGGAGAACTTGAGGGAGAGAA ABBT01000201.1 145128 145177 - 1 11
136368 4e1d326f7ab7d7848d0da902610de7b6 HISTO_DM.Contig933|sl-143031-143077|AS TCTGAACGCAGAGCGAACTACAGTTATCAAAGGCGTATGATACCGGG ABBT01000057.1 143031 143077 - 1 12
136369 81257fdd8b29d365dd577357289dd93e HISTO_DM.Contig933|sl-181977-182026|AS GGCGATCTTTTCTTTGTCAAGCTTTGGATCTAGGGTTCTCGATCATAATC ABBT01000057.1 181977 182026 - 1 13
136370 0cce077848eb8971782fb2891717c8e7 HISTO_DM.Contig940|sl-253719-253760|AS TGCTGCTTCACTCCCCGTCTGCTTGCGTATACTAGTACTCCT ABBT01000060.1 253719 253760 - 1 14
136371 d1110f2c35a0b063e172fff735e591b8 HISTO_DM.Contig933|sl-133627-133668|AS CATCTCCGACTCCCTCGCCTCCTCTCGCTCGTCTCATCGTTC ABBT01000057.1 133627 133668 - 1 15
136372 52c56aa3a59168d2f35bbb1549ec7bca HISTO_DM.Contig933|sl-72992-73041|AS CATGTACAGTACATACATGTACCTGCTGGTTTGATGCTGGCTAGCTAGGC ABBT01000057.1 72992 73041 - 1 16
136373 7ced346b044364bde471c1a56d3b1c86 HISTO_DM.Contig933|sl-45320-45369| TGCGCTCGTTTCAATGTTCAATGGGTTCAATTTTCAACCAACGAAGATGA ABBT01000057.1 45320 45369 + 1 17
136374 5ee879beb42f437007367f77d99b63c6 HISTO_DM.Contig933|sl-247199-247245|AS CGTATTTGACGGTGGAAAATAGTGGTGGTGTTGCCAGGTTGAGATCA ABBT01000057.1 247199 247245 - 1 18
136375 ba4bc0c1871b2a47181b9327f8ce23e8 HISTO_DM.Contig933|sl-203451-203492| CAAGTCAGCGCTCAATGTGCCGTCGTTATCGCCTACGAAAGC ABBT01000057.1 203451 203492 + 1 19
136376 6296a44c88da1fa61733fe04dc859a8c HISTO_JG.Contig206:165907,170425 TEF1|sl-2827-2876|AS GGGAAAACAGGTTTTAACATTTCCCTAAACATATTCTAACTGTCTACCTA ABBT01000140.1 168733 168782 - 1 20

Total number of rows: 12396

Table truncated, full table size 1933 Kbytes.




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