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Platform GPL14017 Query DataSets for GPL14017
Status Public on Aug 12, 2011
Title Histoplasma_capsulatum_G217B_WGTA_026573
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) GSM771266
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
24793 76df025a70d0748672dcaf7c924bd1fd_76df025a70d0748672dcaf7c924bd1fd QC-3prime TGACTGACTGGACTGTGGGTGTGCGATACGTGTCC 1 1
24794 897052f32640e2baa47cc6764a38caa5_897052f32640e2baa47cc6764a38caa5 QC-5prime TGGGTGTGCGATACGTGTCCGACTGACTGACTGAC 1 2
24795 2c61f4bf1b429b0f1c701909ad292a93 HISTO_BP.Contig459|sl-185099-185140|AS GAGGGCAGAACGAACAGGTTCAGTGTCACCAGTGCGGAAGCT ABBT01000035.1 185099 185140 - 1 3
24796 fd5b99ac4fc21b8cdd63a3b8d6252fa8 HISTO_BP.Contig459|sl-356604-356652| CGGTTGAGAAGTTGCCAAATACTCGATTTGCCATCAGATACGCGACAAC ABBT01000035.1 356604 356652 + 1 4
24797 ce59b178dc86a0597f2e10367ba82d95 HISTO_BP.Contig459|sl-226876-226917| GTTACGAGAGCGTAAGGCGTTGGGCGACTCGTGCCAAGATCG ABBT01000035.1 226876 226917 + 1 5
24798 a52267f2b19e9db79cd7c5caa5556beb HISTO_BP.Contig459|sl-252139-252180| CACAGTGCTCTGGCGTACGTGACCCGGCCGCCTATCTGAAAC ABBT01000035.1 252139 252180 + 1 6
24799 65803af474f9b47e7f179f289cb39940 HISTO_BP.Contig459|sl-265522-265570| AGCCGTCATTGAAACAGAAACGGTTGCTCTATGCGTATAGTCTTTAGCA ABBT01000035.1 265522 265570 + 1 7
24800 3ea356f2e7893cb8c5b8315df33dd077 HISTO_BP.Contig459|sl-365804-365851|AS TGGTACCGGTAATAAATTTTCTGGCGACGAGTCGGACAGCAATGTACT ABBT01000035.1 365804 365851 - 1 8
24801 ed5d927635af69e69ead867cdee435f8 HISTO_BP.Contig459|sl-116906-116951| GCATAGTTTAGCGGATTGTTTTGACTGAACAGAGCCCCCCCTCAAT ABBT01000035.1 116906 116951 + 1 9
24802 be84ae3641158000bc22253e97b41697 HISTO_BP.Contig459|sl-313285-313334|AS TTCGATGTCCGATCGCCTGTATATCTAACCATCTACATCCTTTGTCCTGT ABBT01000035.1 313285 313334 - 1 10
24803 1dcdc91d4840003ecacd7c98b1567523 HISTO_BP.Contig459|sl-282796-282841|AS CCGTAATACAGGAACCACGGGCTTTTTGTCGAAATGGTCCTCCATC ABBT01000035.1 282796 282841 - 1 11
24804 82706e6728b9ec07fa3f8206bd9140d6 HISTO_BP.Contig459|sl-243212-243261|AS AGCGTTCCCTTTGTGGCACAGGATTACACCCTCCTTTAGTTAACAAGTAG ABBT01000035.1 243212 243261 - 1 12
24805 bdb4111fe10dbdefbe30862380103ff2 HISTO_BP.Contig459|sl-366625-366670|AS CAGGTGCACTTTCGGGCTATTTCTCAGCCAGCCATAATCATCAGTC ABBT01000035.1 366625 366670 - 1 13
24806 9270b99232292a75b316968e67435f25 HISTO_BP.Contig459|sl-103398-103442| GATTATGGTGATGGAAGAGAAGAATCCCGCCGTAGCGGGGTAGAT ABBT01000035.1 103398 103442 + 1 14
24807 3c042b83114def8f3958171759d574a7 HISTO_BP.Contig459|sl-328439-328484| CGAGAGAAGCTACGAATTGACGAGATACGGGACCGCAGATTTCCAT ABBT01000035.1 328439 328484 + 1 15
24808 85e9d29a33b625eeabe137f65d1c169b HISTO_BP.Contig459|sl-305055-305104|AS CAACACCCGCCTACTAGATTTTGCAAATCGCATGCAGCATACATACAACA ABBT01000035.1 305055 305104 - 1 16
24809 b8493d8f38652128e93bd65dd2695c19 HISTO_BP.Contig459|sl-204566-204610|AS ATGTTCCCAAACCTCTGGATGCCATTGTGGATGCTTGTACCTACG ABBT01000035.1 204566 204610 - 1 17
24810 6e183f1a7b8299ea8885461b965dd439 HISTO_BP.Contig459|sl-336494-336535|AS TCTCTAGTATGGGACATCATCGCGGGAGGGTTTCTGGAAGCT ABBT01000035.1 336494 336535 - 1 18
24811 c1c2c8ad8c14d17863d300c8177825e0 HISTO_BP.Contig459|sl-192715-192757|AS CGGATCTTGACTGGCAATGTCTGCTGGTCAATTCGCGTTGAAG ABBT01000035.1 192715 192757 - 1 19
24812 93a372f8ab27166e807d47c908a0f20d HISTO_BP.Contig459|sl-325820-325866|AS CCAAGCTATTTGCTCTCTCCATTATACGCGATGAAGAAGGGCGGGTA ABBT01000035.1 325820 325866 - 1 20

Total number of rows: 12396

Table truncated, full table size 1936 Kbytes.




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