NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL6904 Query DataSets for GPL6904
Status Public on Jun 30, 2008
Title Schizosaccharomyces pombe transcriptome slide 1
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Schizosaccharomyces pombe
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site
 
Description The Schizosaccharomyces pombe transcriptome microarray is a custom designed genomic tiling array to map RNA transcripts across the entire genome. The array was designed by tiling 60mer oligo probes every 55 nucleotides (5 nucleotide overlap) across the genome. The reverse complement of every probe was also generated. Probes were generated from sequences representing both nuclear and mitochondrial genomes. Sequences from the mating locus (noted as chromosome Mat) were also included. Chromosomal contig sequences from the Sanger Institute dated February 2007 were used as source. The mating locus sequence was assembled from various sources. Oligo probes with strong hybridization signals from a zebra fish promoter tiling array were also included as non-hybridization controls. The array was designed for two 244K slides. The Agilent Design ID is 015048.
 
Contributor(s) Parnell TJ, Cairns BR
Submission date May 27, 2008
Last update date May 02, 2016
Contact name Timothy J Parnell
E-mail(s) timothy.parnell@hci.utah.edu
Organization name Huntsman Cancer Institute
Street address 2000 Circle of Hope
City Salt Lake City
State/province UT
ZIP/Postal code 84112
Country USA
 
Samples (11) GSM294820, GSM294824, GSM294828, GSM294832, GSM294836, GSM977936 
Series (2)
GSE11619 The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping
GSE39701 Zinc-dependent regulation of the adh1 antisense transcript in fission yeast

Data table header descriptions
ID The FeatureNumber in the Agilent extraction file
SPOT_ID Probe name
CONTROL Boolean value indicating whether feature is a control probe
ORGANISM Name of the organism genome from which the probe was derived
CHROMOSOME The name of the chromosome
RANGE_GB Genbank Accession.version (if known)
RANGE_START Start position (if unique)
RANGE_END End position (if unique)
RANGE_STRAND Strand (if unique)
COPYNUMBER Number of perfect matches to the genome
SEQUENCE Sequence of oligo probe

Data table
ID SPOT_ID CONTROL ORGANISM CHROMOSOME RANGE_GB RANGE_START RANGE_END RANGE_STRAND COPYNUMBER SEQUENCE
1 GE_BrightCorner 1
2 DarkCorner 1
3 DarkCorner 1
4 Spo_P101594-R 0 S. pombe chr2 CU329671.1 3 GGAGATACCTCATACTGGATCATGTCAAAAATCTCTGATACTACATATACGTCTTTATAT
5 Spo_P110716-R 0 S. pombe chr2 CU329671.1 510491 510550 - 1 TCTGAAGTCCTTTGACGCTAGGATTGTCAGCAGTATTTGCAAGGTTTCGAGCAGTATTGA
6 Spo_P022386 0 S. pombe chr1 CU329670.1 1231321 1231380 + 1 CACGATTCAGATCACCACTGGCAAAACCTTGATAAGCAATGTCAAAAACTACCAGATGCT
7 Spo_P043768-R 0 S. pombe chr1 CU329670.1 2407331 2407390 - 1 CGTGCTAATTATGAAATGACGAAGGTCGATATAACCATCGTCGCGGCGGTTTAATAACAG
8 Spo_P000762-R 0 S. pombe chr1 CU329670.1 2 GTAAAATTGTTTGAAAATTTCAGAAAATAATTAAATCGGTACTTGAGCTACGAATCGGAT
9 Spo_P041016-R 0 S. pombe chr1 CU329670.1 2255971 2256030 - 1 AAGATGGGCGATGCCATATTTCTTCTGAATGTTGGGGGCCTGAGTGCCTTTTCCAGCACC
10 Spo_P042235-R 0 S. pombe chr1 CU329670.1 2323016 2323075 - 1 AAACATTTAAACATCGACTAATTTTTTCAACATCTGTTTTCACTTTCAAGTATCGACTAC
11 Spo_P105785 0 S. pombe chr2 CU329671.1 239286 239345 + 1 AAGAGACACCACTGCATTCAGAAAGGAACAATTTAGCTGTAAATTGGACAACATTAGGAC
12 Spo_P004128 0 S. pombe chr1 CU329670.1 227131 227190 + 1 TGGAACCAAACTCAAAGTAATACGAGGAGCGAGAATGACCACGCCAGGCGATTCCTTCGA
13 Spo_P038793 0 S. pombe chr1 CU329670.1 2133706 2133765 + 1 AGTTTAGGAATGAAGTTATTTCAACATTTCTTTCTTTCTCTTTCTTAAAAAATAAACTAA
14 Spo_P024942 0 S. pombe chr1 CU329670.1 1371901 1371960 + 1 ATCGTAGCCTGGCTTGGTACAATACTGCCGACAATGCTTGTTACAGGCCGGACATTTTTG
15 Spo_P099663-R 0 S. pombe 3 TACCGCTAGCCAATTTTTATACCACAGCACATATACTTGGTATTGTCATTCACTAATGTT
16 Spo_P049276-R 0 S. pombe 3 ATAGCAATTGTTGCACTAATATCGAAAGGGGACGATTAATTATGTTTTAATAAGATATAG
17 Spo_P040391 0 S. pombe chr1 CU329670.1 2221596 2221655 + 1 GCTTTCCATATCTGTATGGCTGGAGTTCGAACAACTGCAGCAATGTCTTGTCGAACAATG
18 Spo_P095383 0 S. pombe chr1 CU329670.1 5246157 5246216 + 1 AATACCCAATTCCCCCGTGGATATACTTGATGCAAGCGAAGCCTATAAAACTGAGTAAAA
19 Spo_P033699 0 S. pombe chr1 CU329670.1 1853536 1853595 + 1 GGTATGATTATTTCCGCTGCTACTGGTTATTGGGATCATTCTATCATTGATGCTGCTCCG
20 Spo_P075910-R 0 S. pombe chr1 CU329670.1 4175141 4175200 - 1 GCAATAAAAATAGCCCACCAAATGCGTTTACGGATGGTTTTCTCTTCATTGGGTATCTTC

Total number of rows: 243504

Table truncated, full table size 29186 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