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Platform GPL890 Query DataSets for GPL890
Status Public on Jan 02, 2004
Title Agilent-011868 Rat Oligo Microarray G4130A (Feature Number version)
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Rattus norvegicus
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
Catalog number G4130A
 
Description
This microarray contains representative sequences derived from rat RefSeq, high-quality public rat mRNA accessions, homologs to human and mouse RefSeq, EST clusters determined by a leading biopharmaceutical company and the Incyte Zooseq database as well as toxicology markers determined by the National Institute of Environmental Health Sciences (NIEHS) and others. Many of the toxicology markers used in the design of this microarray were released to the public domain for the first time and will be used on this unique microarray product.

Arrays of this design have barcodes that begin with 16011868 or 2511868.

Orientation:
Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software.

The ID column represents the Agilent Feature Extraction feature number.

Rows and columns are numbered as scanned by an Axon Scanner (barcode on the bottom, DNA on the front surface).

To match data scanned on an Axon scanner, use the RefNumber column contained in the Agilent-provided GAL file as the ID_REF column in sample submissions.

*** A different version of this platform with the Agilent Probe names in the ID column is assigned accession number GPL7267.
 
Submission date Jan 02, 2004
Last update date Dec 06, 2012
Organization Agilent Technologies
E-mail(s) cag_sales-na@agilent.com
Phone 877-424-4536
URL http://www.agilent.com
Department
Street address
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Samples (1093) GSM36415, GSM36416, GSM36417, GSM36418, GSM36419, GSM36420 
Series (30)
GSE2015 Intestinal epithelial cells transfected with Ras and treated with TGF-beta-1
GSE2441 Hepatic Gene Expression Changes Throughout the Day in the Fischer Rat
GSE2726 parous and AMV mammary gland before and after MNU treatment
Relations
Alternative to GPL7267

Data table header descriptions
ID Agilent feature number
COL Column
ROW Row
NAME Name
SPOT_ID Spot identifier
CONTROL_TYPE Control type
REFSEQ RefSeqAccession
GB_ACC GenBankAccession
GENE Entrez Gene ID
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
UNIGENE_ID UnigeneID
ENSEMBL_ID EnsemblID
TIGR_ID TIGRID
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
CYTOBAND Cytoband
DESCRIPTION Description
GO_ID GoIDs
SEQUENCE

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE REFSEQ GB_ACC GENE GENE_SYMBOL GENE_NAME UNIGENE_ID ENSEMBL_ID TIGR_ID ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION GO_ID SEQUENCE
1 105 215 BrightCorner BrightCorner pos
2 105 214 NegativeControl NegativeControl neg
3 105 213 XM_233260 A_43_P21252 FALSE XM_233260 XM_233260 313427 Usp24_predicted ubiquitin specific protease 24 (predicted) Rn.74199 ENSRNOT00000007778 ref|XM_233260|ref|XM_001064937|gb|CB546590 chr5:127474724-127474783 rn|5q34 PREDICTED: Rattus norvegicus ubiquitin specific protease 24 (predicted) (Usp24_predicted), mRNA [XM_233260] TGTGTTGGTAATTCACCTGATGAGATTTGGCTTTGACTGGGAGAGTGGACGATCCATCAA
4 105 212 AW919304 A_42_P534203 FALSE AW919304 Rn.24396 TC556152 gb|AW919304|tc|TC556152 chr19:52045902-52045961 rn|19q12 AW919304 EST350608 Rat gene index, normalized rat, norvegicus, Bento Soares Rattus norvegicus cDNA clone RGIFP51 5' end, mRNA sequence [AW919304] TAAATCAGACTTCACACCTGAAGCAAGGGACGCTCAAATTTAAAATCCTCTGCTCCTTTA
5 105 211 CB547437 A_43_P22195 FALSE CB547437 Rn.124702 gb|CB547437 CB547437 AMGNNUC:SRPG2-00026-B12-A srpg2 (10238) Rattus norvegicus cDNA clone srpg2-00026-b12 5', mRNA sequence [CB547437] AGTCACTCACGAAGTCGATCTAGAAGTTCCACCTCATCTTACCGATCAAGAAGCTACTCT
6 105 210 TC554731 A_43_P16421 FALSE TC554731 tc|TC554731 chr12:27892389-27892448 rn|12q13 SUM2_MOUSE (Q8BPG6) Sulfatase modifying factor 2 precursor (C-alpha-formyglycine-generating enzyme 2), partial (21%) [TC554731] TATATATCCACTTCCTCAACTATCAATAACCTTTGGGCCCATACAGAGAAATAGGGCTGG
7 105 209 Pro25G Pro25G pos
8 105 208 NM_130424 A_43_P13118 FALSE NM_130424 156435 Tmprss2 transmembrane protease, serine 2 Rn.81082 gb|NM_130424|gb|AB073550 chr11:37638033-37637974 rn|11q12 Rattus norvegicus transmembrane protease, serine 2 (Tmprss2), mRNA [NM_130424] GO:0004252(serine-type endopeptidase activity)|GO:0006508(proteolysis)|GO:0016021(integral to membrane) TCAGATGTGCTGAATGCTGCCATGGTACCCTTGATCGAGCCCTCCAAATGTAATAGTAAA
9 105 207 XM_223116 A_43_P19445 FALSE XM_223116 Rn.154568 ENSRNOT00000004704 gb|XM_223116|gb|CB605581|ens|ENSRNOT00000004704|ens|ENSRNOT00000000046 chr13:70223579-70214510 rn|13q21 Rattus norvegicus similar to 6820428L09 protein (LOC305101), mRNA [XM_223116] AGGACCTTTGTTCCCAAGCTGGAACCTGTGCTGAGCGCCAAGCATGAGGAAGCCAAGCAT
10 105 206 NM_001014175 A_43_P11302 FALSE NM_001014175 NM_001014175 361990 LOC361990 similar to DKFZP547E1010 protein Rn.15859 ENSRNOT00000017561 TC535427 ref|NM_001014175|ref|XM_001068792|ref|XM_575736|gb|BC100084 chr2:182722112-182722084 rn|2q34 Rattus norvegicus similar to DKFZP547E1010 protein (LOC361990), mRNA [NM_001014175] ATGTCGAAAACTAAAGGACACCTGGATGCTTGAATTGGATGCCTACATGGCACAGACAGA
11 105 205 XM_342271 A_43_P22361 FALSE XM_342271 XM_342271 361975 Lrba_predicted LPS-responsive beige-like anchor (predicted) ENSRNOT00000023418 TC548842 ref|XM_342271|ref|XM_001066755|ref|XM_001066811|ref|XM_001066905 chr2:178247079-178247138 rn|2q34 PREDICTED: Rattus norvegicus LPS-responsive beige-like anchor (predicted) (Lrba_predicted), mRNA [XM_342271] GO:0007165(signal transduction)|GO:0008104(protein localization)|GO:0016023(cytoplasmic membrane-bound vesicle)|GO:0016197(endosome transport)|GO:0051018(protein kinase A binding) TCGAAAAGTGAAGGGATCCGAGTACAGGCACTCAAGGCACTGGGCTACTTTTTAAAACAT
12 105 204 TC541420 A_43_P10152 FALSE TC541420 tc|TC541420 chr9:56777989-56778049 rn|9q31 ACTTTGAGAAGCACAGCTCATGGGGCTCACGCCCTTCGCCACGGTCGGACAAAACCCGGA
13 105 203 NM_012650 A_42_P573643 FALSE NM_012650 NM_012650 24775 Shbg sex hormone binding globulin Rn.37473 ENSRNOT00000015248 TC572903 ref|NM_012650|gb|M15034|gb|BC097336|ens|ENSRNOT00000015248 chr10:56446733-56446372 rn|10q24 Rattus norvegicus sex hormone binding globulin (Shbg), mRNA [NM_012650] GO:0005496(steroid binding)|GO:0005497(androgen binding)|GO:0005515(protein binding)|GO:0005576(extracellular region)|GO:0005615(extracellular space)|GO:0008289(lipid binding)|GO:0009914(hormone transport)|GO:0042803(protein homodimerization activity) ACCCTCAGGGCCATCTCTCCCTTGGGGCTTTACCAGGAGAGGACTCTTCTGCTTCCTTTT
14 105 202 Pro25G Pro25G pos
15 105 201 NM_139105 A_43_P13367 FALSE NM_139105 NM_139105 245964 Rnh1 ribonuclease/angiogenin inhibitor 1 Rn.3756 ENSRNOT00000022241 TC571968 ref|NM_139105|gb|BC070501|ens|ENSRNOT00000022241|ens|ENSRNOT00000041526 chr1:201508732-201508674 rn|1q41 Rattus norvegicus ribonuclease/angiogenin inhibitor 1 (Rnh1), mRNA [NM_139105] GO:0006401(RNA catabolism)|GO:0008428(ribonuclease inhibitor activity) GCTTTGGTTGTCCTAGGGTTGGACTGGCGATAAGCATTGGGATCTTACTTCAGTAGAAAA
16 105 200 CB545584 A_43_P20241 FALSE CB545584 Rn.41244 TC545112 gb|CB545584|tc|TC545112 chr1:263043037-263042985 rn|1q55 CB545584 AMGNNUC:HKR1-00265-A1-A Anemic Rat Kidney (10400) Rattus norvegicus cDNA clone hkr1-00265-a1 5', mRNA sequence [CB545584] ACACCACATACTGGAGCCCAGAATATACCTTCCCGTCTCAGGAGGAGGCTATCCAGTGTG
17 105 199 XM_233713 A_43_P21201 FALSE XM_233713 Rn.140941 ENSRNOT00000023614 gb|XM_233713|gb|CB544431|ens|ENSRNOT00000023614 chr5:172507446-172507387 rn|5q36 Rattus norvegicus similar to Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma) (LOC313767), mRNA [XM_233713] CACGCAGTGCTACATGCACAACAAACATGACCTTACCCATGCCTTTGAGCGCTATGAGAC
18 105 198 A_43_P11033 A_43_P11033 FALSE chr1:085804665-085804724 rn|1q21 AGCGACAGCAAGATGTGATTCCGAGCGTGAAATTTCTTTTCATCTTCAGTCTGTGGACGT
19 105 197 CB545791 A_43_P13501 FALSE CB545791 gb|CB545791 chr7:117211519-117211578 rn|7q34 CB545791 AMGNNUC:NRDG1-00053-D7-A nrdg1 (10855) Rattus norvegicus cDNA clone nrdg1-00053-d7 5', mRNA sequence [CB545791] ACTCAGCTTGCTCTGTCTTTGGTTGGAAGACTTTGGGGGAAGTTCTTTTCCACTTCTGCC
20 105 196 A_43_P22765 A_43_P22765 FALSE chr10:011888316-011888375 rn|10q12 GCCAAGAACTAGGAAAGGACGCAGTGGCCAGGACACACTAAAATAATGTCATGCTACCGG

Total number of rows: 22575

Table truncated, full table size 9188 Kbytes.






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Supplementary file Size Download File type/resource
GPL890_old_annotations.txt.gz 2.8 Mb (ftp)(http) TXT

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