NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL17848 Query DataSets for GPL17848
Status Public on Oct 30, 2013
Title NimbleGen Rat Promoter Array [2006-10-31_RN34_promoter_1of2]
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Rattus norvegicus
Manufacturer NimbleGen
Manufacture protocol See manufacturer's website (www.nimblegen.com).
 
Description Design ID: 4808
Design name: 2006-10-31_RN34_promoter_1of2
Genome build: RN34

First of two arrays in the consolidated promoter region design for the rat genome (rn34). Array one contains promoter regions from chromosomes 1 through 7 (through position 138518067).
Includes 4500 bp upstream of transcriptional start and 1125 bp downstream. Isothermal probes using dual tm/cycle restriction:, 50-75 bp, tm 76, 148 cycles, 15-mer frequency of 100. Probes selected from rn34_tiling database using interval of 75 bp and window size of 25 bp. Interval spacing: 104 bp (mean); 105 bp (median).
 
Submission date Oct 28, 2013
Last update date Oct 30, 2013
Contact name Deborah Anderson
E-mail(s) deborah.anderson@saskcancer.ca
Phone 13069667038
Organization name University of Saskatchewan
Street address 107 Wiggins Road
City Saskatoon
State/province Saskatchewan
ZIP/Postal code S7N 5E5
Country Canada
 
Samples (1) GSM1252957
Series (2)
GSE51802 Association of CREB3L1 with promoters in LN4D6 CREB3L1 cells
GSE51857 CREB3L1 is a metastasis suppressor that represses expression of genes regulating metastasis, invasion and angiogenesis

Data table header descriptions
ID PROBE_ID
SEQ_ID
CHROMOSOME Chromosome
RANGE_GB RefSeq accession.version of CHROMOSOME (RN34)
RANGE_START Start coordinate relative to RANGE_GB; POSITION
LENGTH Probe length
SEQUENCE Probe sequence

Data table
ID SEQ_ID CHROMOSOME RANGE_GB RANGE_START LENGTH SEQUENCE
CHR01P000259513 chr1:259488-265113 chr1 NC_005100.2 259513 58 TTTACTGATATATTCTAGAATATTCGTGACAAAACTGTATGTTCTAGAAACCAGCTTT
CHR01P000259708 chr1:259488-265113 chr1 NC_005100.2 259708 50 GCAGCATACCTATAAATGCATGGGGTCCAAGTTTTCTTGTAGGCACATGC
CHR01P000259808 chr1:259488-265113 chr1 NC_005100.2 259808 55 TGGTGCCCTTGAATTAACTGAAAGTTTTAAGGAAGTTTTCCATGATGGTCCTGTA
CHR01P000259903 chr1:259488-265113 chr1 NC_005100.2 259903 59 TAAGTAGATCGAAATAATTGTTTTGATGTAAATATGCTTTATCCAGAACTCCCATTGTA
CHR01P000260013 chr1:259488-265113 chr1 NC_005100.2 260013 60 AGATAAGGATTCTTGTTGATCTCATCAGTTGCAAATAACAATACCAGAAAAAACTCATAT
CHR01P000260093 chr1:259488-265113 chr1 NC_005100.2 260093 57 CAAGCATAATGATGTGAAGGGAGACGTATGAAAAATAAAATTTCAATTGTAGTTAAG
CHR01P000260209 chr1:259488-265113 chr1 NC_005100.2 260209 58 ATTAGAGATCTTAATATTTGAATACAACTTAATAATTCATAGACCTAGGATACTAATC
CHR01P000260299 chr1:259488-265113 chr1 NC_005100.2 260299 61 AGAGGACTATTTTATCTCTGAATACAATCTTCAAGCCACATTAGAGTCCAATTGAGTAAGA
CHR01P000260389 chr1:259488-265113 chr1 NC_005100.2 260389 62 TCCACCAATGCAAATAACAAGCATGACTTAAACCACACATGAAATACAAAACATATTTGCAC
CHR01P000260504 chr1:259488-265113 chr1 NC_005100.2 260504 58 ATATTTTGCAAATCATAGATTACATCAAAAATTTTTGTTCAACTTTTACATTCATATA
CHR01P000260599 chr1:259488-265113 chr1 NC_005100.2 260599 59 ATGTTTATTACTCATGATTGTATATCAAATGTTGAATAGTAAATTGTTTCAAAACTCAA
CHR01P000260689 chr1:259488-265113 chr1 NC_005100.2 260689 57 AGCATGAAGAATTCAAAGGTAAATCATTTAGAAATATATTCAAAAGCCCTTATATAA
CHR01P000260889 chr1:259488-265113 chr1 NC_005100.2 260889 62 TAAAGAATGGTAGTGGGTCAATCATGGACATACTGCATAGATGTATGAAATACCCATTAACT
CHR01P000261089 chr1:259488-265113 chr1 NC_005100.2 261089 53 GATTTTATGATGAAACTCTTGGCTCCTTTTAAATTTTGAACTTATTTGGTTAA
CHR01P000261210 chr1:259488-265113 chr1 NC_005100.2 261210 62 TCACTGTGCATGATATATATCCATGTAAATAGGTCATTTTGGAGTTTTGCGGTATAGAAAAC
CHR01P000261410 chr1:259488-265113 chr1 NC_005100.2 261410 51 CATTTCCTGAGACTCTACTTGTTGAAAAATGAGTTCGTGATAGGTGTGGGC
CHR01P000261505 chr1:259488-265113 chr1 NC_005100.2 261505 57 GGACCATGTCAAATGTGTGCTGTGTTAACCATTCCATTGGGTTTTTCAACATAAAAA
CHR01P000261595 chr1:259488-265113 chr1 NC_005100.2 261595 60 AGTTAAAATGATTCCACTGCCCCATAGACTGAGAAATATCTACTGGATACTTGGATGTGT
CHR01P000261700 chr1:259488-265113 chr1 NC_005100.2 261700 51 GGTGGGCAAAAATGACAGTCCCGTGGAAGAAATCAAGGCTGAAATCTTTAT
CHR01P000261795 chr1:259488-265113 chr1 NC_005100.2 261795 63 CGTGCAACTAAATATGTCCATCTTGCAAAGTTGAGTTCTAGAGTGGAGATCATTTTGCCATAA

Total number of rows: 388899

Table truncated, full table size 46864 Kbytes.




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

Supplementary file Size Download File type/resource
GPL17848_2006-10-31_RN344_promoter_1of2.ndf.gz 25.0 Mb (ftp)(http) NDF
GPL17848_2006-10-31_RN344_promoter_1of2.pos.gz 3.2 Mb (ftp)(http) POS

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap