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Platform GPL14033 Query DataSets for GPL14033
Status Public on Aug 12, 2011
Title Histoplasma_capsulatum_G217B_WGTA_027127
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) GSM771282
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
222305 76df025a70d0748672dcaf7c924bd1fd_76df025a70d0748672dcaf7c924bd1fd QC-3prime TGACTGACTGGACTGTGGGTGTGCGATACGTGTCC 1 1
222306 897052f32640e2baa47cc6764a38caa5_897052f32640e2baa47cc6764a38caa5 QC-5prime TGGGTGTGCGATACGTGTCCGACTGACTGACTGAC 1 2
222307 23d8a04dd639312d0f6094aab759f941 HISTO_ZL.Contig1161c|sl-342390-342431| TTCCGAAGAAGTCGTTATCCCTCCAGCCCTGTGGATACCGAT ABBT01000205.1 1148364 1148405 + 1 3
222308 79b76337e4b47a6353f1bc2649e6ceab HISTO_ZL.Contig1161c|sl-187077-187119|AS ACCGCCTCCCCCATACCGCACTTTCTTTTTTCTTGGAATCTCT ABBT01000205.1 993051 993093 - 1 4
222309 eedc20c3ee1139719ef8a89e5f1b969b HISTO_ZL.Contig1161c|sl-183185-183226| CAGGAGCGAGCAGATGGGTTGGTGGGAACGGGACATGTTTTT ABBT01000205.1 989159 989200 + 1 5
222310 b8805ecb6ee3647e27382a2f381078e0 HISTO_ZL.Contig1161d|sl-42284-42325| CTGTTGCCTTTGCCGCCCATGCACCCAACACGCGTTTATGTA ABBT01000205.1 1251245 1251286 + 1 6
222311 e5eb1286cae19ccb9346f6f47c2e4bc1 HISTO_ZL.Contig1161c|sl-184090-184131|AS GCCAGTGATATCGACTTTGGCGCTCTCAACCGTCACAGGAAA ABBT01000205.1 990064 990105 - 1 7
222312 4644c4f70156d571dea54783f4251d86 HISTO_ZL.Contig1161d|sl-44660-44703|AS ACTCTTCACCATCTGTCTCTTCAACCTCCTCACCCTCACCACAG ABBT01000205.1 1253621 1253664 - 1 8
222313 01a3f46be0ba709808e162100f497810 HISTO_ZL.Contig1161c|sl-279084-279125|AS AACTCTTGGGTGCACGAAAGCCGCTCTCGCCCAGCATATGTT ABBT01000205.1 1085058 1085099 - 1 9
222314 5a6e4fbfcaa3fb402a1614f0879f1b36 HISTO_ZL.Contig1161c|sl-226056-226104| GCGGGCTCCCTATTATGTGTAATTTGTAAAAGCTTGATGGCCGAATCGG ABBT01000205.1 1032030 1032078 + 1 10
222315 5a7e0f760fce569584fe45e9bb0311c2 HISTO_ZL.Contig1161c|sl-244849-244892|AS GCGATGGAAAAGACTTCTTTTCCGAGAATGAGACGGCGAAGCCT ABBT01000205.1 1050823 1050866 - 1 11
222316 3596cdadc21b5b29f46e11722453dc37 HISTO_ZL.Contig1161c|sl-314807-314849|AS CACCACTCACTTCCCCCACCACGCCCAGAACGCCGCCTCACTG ABBT01000205.1 1120781 1120823 - 1 12
222317 91d18be06be31f8637302aafc4b4ed51 HISTO_ZL.Contig1161c|sl-378799-378848|AS AAGACAGAAATAATGATCTTTTTAAGGAAAACGTAACCCCTCGGCTAGCT ABBT01000205.1 1184773 1184822 - 1 13
222318 a8f442007799c3ed96a85167b01aed71 HISTO_ZL.Contig1161c|sl-357786-357827|AS CTGTATGTTCGATGTCCCCATACGAAGTGGAGACCACGCTGG ABBT01000205.1 1163760 1163801 - 1 14
222319 379d94cca33cebc9d4f22f197c8d6e11 HISTO_ZL.Contig1161d|sl-3251-3294|AS ATACGTACAGCCTCTGCAAAACCGTGGCGGAAATTTCATGGAGA ABBT01000205.1 1212212 1212255 - 1 15
222320 5743fefc91c1a6051e845d86b98a41b7 HISTO_ZL.Contig1161d|sl-52200-52249| CGTTCCATGTTAAATATATATTCCGGTTCCAGCAGGGTTGTCGGGGTACA ABBT01000205.1 1261161 1261210 + 1 16
222321 b481bd395c2cba1b2c11968fe44bd5ba HISTO_ZL.Contig1161d|sl-8806-8855| AGATGAGTGTGCTTCATTCTGATCTTTATGTCACTCATCGATCAATTGCC ABBT01000205.1 1217767 1217816 + 1 17
222322 77be57b17c8ab5e39920be5c20398f2b HISTO_ZL.Contig1161c|sl-385455-385496| TTTCTATCTGAACCCCCAGTGTCGCTGCCGTCACCTCACATC ABBT01000205.1 1191429 1191470 + 1 18
222323 e0bd6f65dc1dbea2e9ce7b69daf8aefb HISTO_ZL.Contig1161c|sl-232336-232382| ACCTATAAAGTCATCTCACCAACAGGGCTGGCTTATCCCCTGACTTG ABBT01000205.1 1038310 1038356 + 1 19
222324 ec3026781eea6193ebceffb879545146 50mer_control_AS CAAACAACCTTCCGGAGCACTCTTTGATGTTAGGTGATTGGCAAGAAGTT 1 20

Total number of rows: 12396

Table truncated, full table size 1987 Kbytes.




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