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Platform GPL6543 Query DataSets for GPL6543
Status Public on Mar 03, 2008
Title [RaEx-1_0-st] Affymetrix Rat Exon 1.0 ST Array [transcript (gene) version]
Technology type in situ oligonucleotide
Distribution commercial
Organism Rattus norvegicus
Manufacturer Affymetrix
Manufacture protocol See manufacturer's web site
 
Description Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html

#%create_date=Mon Mar 16 20:01:52 2009 PDT
#%chip_type=RaEx-1_0-st-v1
#%lib_set_name=RaEx-1_0-st
#%lib_set_version=v1
#%genome-species=Rattus norvegicus
#%genome-version=rn4
#%genome-version-ucsc=rn4
#%genome-version-ncbi=HGSC v3.4
#%genome-version-create_date=2004-11
#%netaffx-annotation-date=2009-03-16
#%netaffx-annotation-netaffx-build=28
 
Web link http://www.affymetrix.com/support/technical/byproduct.affx?product=raexon-st
http://www.affymetrix.com/analysis/index.affx
Submission date Mar 03, 2008
Last update date Jun 03, 2009
Organization Affymetrix, Inc.
E-mail geo@ncbi.nlm.nih.gov, support@affymetrix.com
Phone 888-362-2447
URL http://www.affymetrix.com/index.affx
Street address
City Santa Clara
State/province CA
ZIP/Postal code 95051
Country USA
 
Samples (205) GSM318214, GSM318215, GSM318216, GSM318217, GSM318218, GSM318219 
Series (16)
GSE12670 Renal gene expression analysis: transcript-level data
GSE12672 Renal gene expression analysis of rat malignant hypertensive end-organ damage
GSE19175 Differential gene expression in lactating rats compared against age matched virgin controls
Relations
Affiliated with GPL6194

Data table header descriptions
ID transcript_cluster_id
GB_LIST GenBank and RefSeq Accessions from mrna_assignment column
SPOT_ID genomic location of the transcript cluster in the version of the genome assembly used at annotation time. Coordinates are standard 1-based (length=stop-start+1).
seqname chromosome number
RANGE_GB NCBI RefSeq for chromosome of current build
RANGE_STRAND strand (+|-)
RANGE_START start (integer). Coordinates are standard 1-based (length=stop-start+1).
RANGE_STOP stop (integer). Coordinates are standard 1-based (length=stop-start+1).
total_probes Total number of probes contained by this transcript cluster
gene_assignment Gene information for each assigned mRNA for mRNAs that corresponds to known genes
mrna_assignment Description of the public mRNAs that should be detected by the sets within this transcript cluster based on sequence alignment
category Array design category of the transcript cluster

Data table
ID GB_LIST SPOT_ID seqname RANGE_GB RANGE_STRAND RANGE_START RANGE_STOP total_probes gene_assignment mrna_assignment category
7024575 NM_001099462 chr1:5526-17480 chr1 NC_005100.2 + 5526 17480 47 NM_001099462 // Vom2r5 // vomeronasal 2 receptor, 5 // 1p13 // 679691 /// ENSRNOT00000046204 // Vom2r2 // vomeronasal 2 receptor, 2 // 1p13 // 292438 NM_001099462 // RefSeq // Rattus norvegicus vomeronasal 2 receptor, 5 (Vom2r5), mRNA. // chr1 // 100 // 9 // 4 // 4 // 0 /// ENSRNOT00000046204 // ENSEMBL // vomeronasal 2 receptor 2 gene:ENSRNOG00000023718 // chr1 // 100 // 9 // 4 // 4 // 0 /// ENSRNOT00000044270 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:5473:16844:1 gene:ENSRNOG00000021490 // chr1 // 100 // 72 // 34 // 34 // 0 /// ENSRNOT00000049921 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:5526:16968:1 gene:ENSRNOG00000021490 // chr1 // 100 // 72 // 34 // 34 // 0 /// ENSRNOT00000044505 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:8268:16850:1 gene:ENSRNOG00000021490 // chr1 // 100 // 64 // 30 // 30 // 0 main
7024576 chr1:77595-155820 chr1 NC_005100.2 + 77595 155820 68 --- ENSRNOT00000044270 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:5473:16844:1 gene:ENSRNOG00000021490 // chr1 // 100 // 12 // 8 // 8 // 0 /// ENSRNOT00000049921 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:5526:16968:1 gene:ENSRNOG00000021490 // chr1 // 100 // 12 // 8 // 8 // 0 main
7024577 chr1:123829-124007 chr1 NC_005100.2 + 123829 124007 4 --- --- main
7024578 chr1:188050-193243 chr1 NC_005100.2 + 188050 193243 9 --- --- main
7024579 chr1:200688-200725 chr1 NC_005100.2 + 200688 200725 2 --- --- main
7024580 chr1:209209-209370 chr1 NC_005100.2 + 209209 209370 8 --- --- main
7024581 chr1:212472-212593 chr1 NC_005100.2 + 212472 212593 4 --- --- main
7024582 chr1:212740-212805 chr1 NC_005100.2 + 212740 212805 4 --- --- main
7024583 NM_001099654 chr1:212902-315423 chr1 NC_005100.2 + 212902 315423 32 NM_001099654 // Vom2r65 // vomeronasal 2 receptor, 65 // 14p22 // 689403 NM_001099654 // RefSeq // Rattus norvegicus vomeronasal 2 receptor, 65 (Vom2r65), mRNA. // chr1 // 100 // 13 // 4 // 4 // 0 main
7024584 chr1:297344-297566 chr1 NC_005100.2 + 297344 297566 4 --- --- main
7024585 chr1:297578-298190 chr1 NC_005100.2 + 297578 298190 4 --- --- main
7024586 chr1:298191-298244 chr1 NC_005100.2 + 298191 298244 1 --- --- main
7024587 NM_001099461 chr1:298245-761491 chr1 NC_005100.2 + 298245 761491 80 NM_001099461 // Vom2r1 // vomeronasal 2 receptor, 1 // 1p13 // 678740 /// ENSRNOT00000044213 // Vom2r3 // vomeronasal 2 receptor, 3 // 1p13 // 502213 /// ENSRNOT00000041455 // Vom2r1 // vomeronasal 2 receptor, 1 // 1p13 // 678740 /// ENSRNOT00000046204 // Vom2r2 // vomeronasal 2 receptor, 2 // 1p13 // 292438 NM_001099461 // RefSeq // Rattus norvegicus vomeronasal 2 receptor, 1 (Vom2r1), mRNA. // chr1 // 100 // 3 // 3 // 2 // 0 /// ENSRNOT00000044213 // ENSEMBL // vomeronasal 2 receptor 3 gene:ENSRNOG00000040335 // chr1 // 75 // 5 // 3 // 4 // 0 /// ENSRNOT00000041455 // ENSEMBL // vomeronasal 2 receptor 1 gene:ENSRNOG00000032583 // chr1 // 100 // 3 // 3 // 2 // 0 /// ENSRNOT00000046204 // ENSEMBL // vomeronasal 2 receptor 2 gene:ENSRNOG00000023718 // chr1 // 100 // 3 // 3 // 2 // 0 main
7024588 chr1:298572-298945 chr1 NC_005100.2 + 298572 298945 4 --- --- main
7024589 chr1:303238-303282 chr1 NC_005100.2 + 303238 303282 4 --- --- main
7024590 chr1:303283-303314 chr1 NC_005100.2 + 303283 303314 4 --- --- main
7024591 chr1:303315-303509 chr1 NC_005100.2 + 303315 303509 4 --- --- main
7024592 chr1:311499-311643 chr1 NC_005100.2 + 311499 311643 4 --- ENSRNOT00000050719 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:951015:972300:-1 gene:ENSRNOG00000029249 // chr1 // 100 // 100 // 4 // 4 // 0 /// ENSRNOT00000043301 // ENSEMBL // cdna:known chromosome:RGSC3.4:1:951015:972441:-1 gene:ENSRNOG00000029249 // chr1 // 100 // 100 // 4 // 4 // 0 main
7024593 chr1:392255-435408 chr1 NC_005100.2 + 392255 435408 46 --- ENSRNOT00000041173 // ENSEMBL // cdna:novel chromosome:RGSC3.4:9:112742951:112743333:1 gene:ENSRNOG00000029305 // chr1 // 100 // 7 // 3 // 3 // 0 /// ENSRNOT00000048288 // ENSEMBL // cdna:novel chromosome:RGSC3.4:9:112858222:112861105:1 gene:ENSRNOG00000031291 // chr1 // 25 // 17 // 2 // 8 // 1 main
7024594 chr1:399606-399684 chr1 NC_005100.2 + 399606 399684 4 --- --- main

Total number of rows: 361289

Table truncated, full table size 73234 Kbytes.




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