NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL14022 Query DataSets for GPL14022
Status Public on Aug 12, 2011
Title Histoplasma_capsulatum_G217B_WGTA_026583
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) GSM771271
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
86773 76df025a70d0748672dcaf7c924bd1fd_76df025a70d0748672dcaf7c924bd1fd QC-3prime TGACTGACTGGACTGTGGGTGTGCGATACGTGTCC 1 1
86774 897052f32640e2baa47cc6764a38caa5_897052f32640e2baa47cc6764a38caa5 QC-5prime TGGGTGTGCGATACGTGTCCGACTGACTGACTGAC 1 2
86775 8d0c62cfa3f3092fccb03fe0f2b2bfc5 HISTO_ZE.Contig158|sl-130147-130196| ACCTCAGTAAGTGACTCTGCTGATAGACATTGCAGAATACATGCATACCG ABBT01000195.1 130147 130196 + 1 3
86776 eee8ef407b5bd47b8561ea5a32047796 HISTO_ZE.Contig158|sl-102950-102999|AS GCACATGGTATTACAACATACTTTTTATATAGCAGCATCTTTTATGCCGG ABBT01000195.1 102950 102999 - 1 4
86777 cb33ae6dc24ed242c6165956def6c452 HISTO_ZE.Contig158|sl-131092-131133| GGTTAGTGGCCGACAAGGTCCCGACTCCAACTATCCTGTTTG ABBT01000195.1 131092 131133 + 1 5
86778 c0195d8096dbc2891371a0a8585f229f HISTO_ZE.Contig158|sl-224186-224227|AS CGGATCGCTATGATTGCCGACTTTGTGCCAGGCAATCCACTT ABBT01000195.1 224186 224227 - 1 6
86779 18a76ef5fc37fd943e904cdcb28a6595 HISTO_ZE.Contig158|sl-209027-209076|AS GCGGAGATCTACAACGAGGAGAACGAGGACAGCTTTCTGGTCTATATCAA ABBT01000195.1 209027 209076 - 1 7
86780 626bc538e2c261eb48977aadc9ad1e62 HISTO_ZE.Contig158|sl-237625-237666|AS CACCCACCCCTAACTCATCGGGCGACAGTTGCTGCAGAACTA ABBT01000195.1 237625 237666 - 1 8
86781 f1faf80290e0014081ff0b553530c609 HISTO_ZL.Contig1117:143635,146491 CBP1|sl-630-678|AS TCGACAGGACAAAGATAGAGAGATCTCTGGATCCCAAGGTTAAAAGCAA ABBT01000201.1 144264 144312 - 1 9
86782 e3d81dcfceb88fec93fb8f22799cb003 HISTO_ZE.Contig158|sl-284646-284695| CCGCAACAGCCTGAATCCAAGAGAGTATATTCTTACTCAGGAAGGTGTCC ABBT01000195.1 284646 284695 + 1 10
86783 4efbdd55548f2eb418e385e3992f73c4 HISTO_ZE.Contig158|sl-223996-224037|AS CGACAAACTTCATTGGCCCATTCAACTCGGAGGCCAAGTTCG ABBT01000195.1 223996 224037 - 1 11
86784 cb13e3e68f08f1b8a4c32d8809c44647 HISTO_ZE.Contig158|sl-235366-235411| GGATACGAAATATCGACAAGAAGCGCAGATTCGGGAAATGCTCCGC ABBT01000195.1 235366 235411 + 1 12
86785 3be7b6540114c600bf1186f55e7f4ad1 HISTO_ZE.Contig158|sl-87024-87065|AS GAAATTATCTGTATTGGGGCGGTCGGGGACATGCGGTTGTGG ABBT01000195.1 87024 87065 - 1 13
86786 64898011e5dda570590aa6771e96431a HISTO_ZE.Contig158|sl-109701-109750|AS TGCCTGATCCTGGAATTCCATGAATCCATAAAAGACCGTGTCCTCCAAAA ABBT01000195.1 109701 109750 - 1 14
86787 01385c43df86a48cf710bf56d9951a60 HISTO_ZE.Contig158|sl-230359-230408|AS GGTTATTCCCAGAAAATGGAAACAACTTGACAACAAAACAATTCGGAAGG ABBT01000195.1 230359 230408 - 1 15
86788 05918edfc5dc1accd3d847808cf3c0df HISTO_ZE.Contig158|sl-266195-266236| CTCTGTCCCGGTATACATCGACAACAGTCGGCGCCCGAACTC ABBT01000195.1 266195 266236 + 1 16
86789 6e38c87e14c1756a98d5376a8aecad5e HISTO_ZE.Contig158|sl-72866-72908|AS CTTAGTAAGGGCGTCCAGAGCGGCTGGGTCCATCATCATGCCA ABBT01000195.1 72866 72908 - 1 17
86790 1726b370ad5bb6cd0a210d35c387be5a HISTO_ZE.Contig158|sl-60821-60868|AS GAGCTCATTGTTTCGAGTTCTGCGTCGTTGAAAAGGCGATGTTGAGAA ABBT01000195.1 60821 60868 - 1 18
86791 48100509ca68283b9c4ba9febdb83672 HISTO_ZE.Contig158|sl-234752-234801| TGGTGTTAGTCATCTCTATCTCTCAACGAACATTCTGTTCTCCCTCCTCA ABBT01000195.1 234752 234801 + 1 19
86792 762b5ced457299b040b630b97f3fd243 HISTO_ZE.Contig158|sl-135009-135055| GGAGCTAACAACTAGACCTAGCCAAATATCTCCCCAGGGCATCTTCC ABBT01000195.1 135009 135055 + 1 20

Total number of rows: 12396

Table truncated, full table size 1925 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap