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Platform GPL17849 Query DataSets for GPL17849
Status Public on Oct 30, 2013
Title NimbleGen Rat Promoter Array [2006-10-31_RN34_promoter_2of2]
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: 4809
Design name: 2006-10-31_RN34_promoter_2of2
Genome build: RN34

Second of two arrays in the consolidated promoter region design for the rat genome (rn34). Array two contains promoter regions from chromosomes 7 (through position 138512442) through chr20, chrX and the "random" chromosomes.
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
 

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
CHR10P000003311 chr10:1-5626 chr10 NC_005109.2 3311 50 AAAACAGTAGCCACAGAAGAGTCATCCTCATGGAGCTGGAGCGCGTGAGA
CHR10P000003416 chr10:1-5626 chr10 NC_005109.2 3416 50 TTCTTGTTTTGATTGGGGAGAGGGAGTGGTAGAAAACCACTAGCAATCAC
CHR10P000003501 chr10:1-5626 chr10 NC_005109.2 3501 50 GACAATGAAACTGCAGGCACTGCTAGTCTCCAGAGGCACCATGTCCCACA
CHR10P000003601 chr10:1-5626 chr10 NC_005109.2 3601 51 ACTAGATACATTGTTCCACAGGTAAGAGTCAAGAACCACGGACAGTCTTCT
CHR10P000003701 chr10:1-5626 chr10 NC_005109.2 3701 60 ATGAATCCTTTACTGAACATGTGTGACAATTTATGGATATTCCTGTTGATAGTAACAACT
CHR10P000003826 chr10:1-5626 chr10 NC_005109.2 3826 62 TAAAATATAAAAGCTTACATAGATGCTGTATTTGTCAGATATAGTTAGGTATGTCCTGAAGA
CHR10P000003926 chr10:1-5626 chr10 NC_005109.2 3926 50 AGAATGCTAAAGAATGGAAAGTCCCTGCCTATGCTATGGCAAGTGCTTGA
CHR10P000004011 chr10:1-5626 chr10 NC_005109.2 4011 52 AAAGTCAACTGAATGACCTTGAGCAACACCACTGTAAAGGAGCAATGAGTCA
CHR10P000004111 chr10:1-5626 chr10 NC_005109.2 4111 51 GAGCTGGAGAGTTCTTTCATAAGCAATTGGACCTTTGATAGAGCTTGCTCT
CHR10P000004211 chr10:1-5626 chr10 NC_005109.2 4211 50 TGTGGGCTTGTCAGATGTCAGAACAATACAGAAAAACTGTCAGGACTCAG
CHR10P000004321 chr10:1-5626 chr10 NC_005109.2 4321 57 CTAGCTAGGTAGAATGACACAGAAAGAGCTTTCTAACGTGCTAGCAGTTTAGTTGTA
CHR10P000004411 chr10:1-5626 chr10 NC_005109.2 4411 50 CTCTTGAGTGAGCTAGCAGGGTTGGAACTCAGTTTACGGCTCTCATTTCT
CHR10P000004521 chr10:1-5626 chr10 NC_005109.2 4521 68 TCTCATTCTTCAGCATATTTACAATACATTGACAGTATATGAAGAAGTATCTAATTATCAGCTCACAA
CHR10P000004606 chr10:1-5626 chr10 NC_005109.2 4606 63 CTTACTGTATCAGATAACTTGATCCTCATTGTGATGGTGTCAGTTGATTCTCCTTTACAGACA
CHR10P000004711 chr10:1-5626 chr10 NC_005109.2 4711 50 ATGCATGCATGTTGAAAGAGGCATTATAAAGAAAGATGAGGGGGGCTGGG
CHR10P000005105 chr10:1-5626 chr10 NC_005109.2 5105 58 GAATGACTGGGTAGCTTTCATCCATTAGCGGTGTAACATAAAGGAGGACAGTTTATTA
CHR10P000005220 chr10:1-5626 chr10 NC_005109.2 5220 58 TAGACATAGTTTATCTTTGTAGTCCAACTCAAAAGAACTCACAGTCCTCCTACCTCAG
CHR10P000005305 chr10:1-5626 chr10 NC_005109.2 5305 59 GCAACACCAAGTCTGGATGGGAAAAAAAGTGAATGTAATTAGCCATAGAGCACATTAAA
CHR10P000036157 chr10:36148-41773 chr10 NC_005109.2 36157 50 ACTCAAGTAGCTCTGGCACACAGAAAGGATTCTAGGAAAGGTCTGTTGAC
CHR10P000036252 chr10:36148-41773 chr10 NC_005109.2 36252 50 TCCCAAACACTATACCCTGGAACCATCAACAAAGCTCCCCCTTTCCCACC

Total number of rows: 388852

Table truncated, full table size 46747 Kbytes.




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Supplementary file Size Download File type/resource
GPL17849_2006-10-31_RN34_promoter_2of2.ndf.gz 25.1 Mb (ftp)(http) NDF
GPL17849_2006-10-31_RN34_promoter_2of2.pos.gz 3.2 Mb (ftp)(http) POS

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