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Platform GPL17864 Query DataSets for GPL17864
Status Public on Nov 21, 2013
Title Agilent-044804 Custom Mouse Coding and LncRNA array 028005 (Feature Number version)
Technology type in situ oligonucleotide
Distribution commercial
Organism Mus musculus
Manufacturer Agilent Technologies
Manufacture protocol see manufacturer's web site at http://www.agilent.com/
 
Description SurePrint G3 Mouse GE 8x60K Microarray customized by Vikram
The Agilent eArray platform was used to customize the SurePrint G3 Mouse GE 8x60K microarray to add 3 custom-designed probes (60nt length) each against several categories of genes, namely pseudogene, genes with small RNA overlap, low stringency lncRNAs and high stringency lncRNAs.
Arrays of this design have barcodes that begin with 16044804 or 2544804.

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.
 
Submission date Oct 30, 2013
Last update date Nov 21, 2013
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Samples (19) GSM1254757, GSM1254758, GSM1254759, GSM1254760, GSM1254761, GSM1254762 
Series (2)
GSE51892 Long noncoding RNA expression in several hematopoietic progenitor and differentiated cell populations using a custom Agilent microarray
GSE52555 Long noncoding RNA expression in several hematopoietic progenitor and differentiated cell populations

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 GenBank Accession number
LOCUSLINK_ID LocuslinkID
GENE_SYMBOL Gene Symbol
GENE_NAME Gene Name
UNIGENE_ID UnigeneID
ENSEMBL_ID EnsemblID
ACCESSION_STRING Accession String
CHROMOSOMAL_LOCATION Chromosomal Location
CYTOBAND Cytoband
DESCRIPTION Description
GO_ID GoIDs
SEQUENCE Sequence

Data table
ID COL ROW NAME SPOT_ID CONTROL_TYPE REFSEQ GB_ACC LOCUSLINK_ID GENE_SYMBOL GENE_NAME UNIGENE_ID ENSEMBL_ID ACCESSION_STRING CHROMOSOMAL_LOCATION CYTOBAND DESCRIPTION GO_ID SEQUENCE
1 192 328 GE_BrightCorner CONTROL pos
2 192 326 DarkCorner CONTROL pos
3 192 324 DarkCorner CONTROL pos
4 192 322 A_55_P2069217 A_55_P2069217 FALSE NM_025385 NM_025385 66151 Prr13 proline rich 13 Mm.393955 ENSMUST00000164688 ref|NM_025385|ref|NM_001170911|ens|ENSMUST00000164688|ens|ENSMUST00000164957 chr15:102291090-102291149 mm|15qF3 Mus musculus proline rich 13 (Prr13), transcript variant 1, mRNA [NM_025385] GO:0003674(molecular_function)|GO:0005634(nucleus)|GO:0005730(nucleolus)|GO:0006351(transcription, DNA-dependent)|GO:0006355(regulation of transcription, DNA-dependent)|GO:0008150(biological_process) GACTCGGAAGAAAATGAAGAAAGCTCATAAGAAGTCGCACAAGCATCACAAGCACGGGAA
5 192 320 A_55_P2062024 A_55_P2062024 FALSE AK053725 21463 Tcp11 t-complex protein 11 ENSMUST00000072628 ens|ENSMUST00000072628|gb|AK053725|tc|TC1585380|riken|E130302P05 chr17:28213666-28213607 mm|17qA3.3 t-complex protein 11 [Source:MGI Symbol;Acc:MGI:98544] [ENSMUST00000072628] GO:0007275(multicellular organismal development)|GO:0007283(spermatogenesis)|GO:0016020(membrane)|GO:0016021(integral to membrane)|GO:0030154(cell differentiation) ATGAGGAAGAGGTAGGGGAAAGCTTTTTTCTTTTTTGGGTGGGGGACAACTTTATTCTTG
6 192 318 A_55_P2259500 A_55_P2259500 FALSE XM_003085392 XM_003085392 319377 D130012P04Rik RIKEN cDNA D130012P04 gene Mm.483805 ref|XM_003085392|ref|XM_003085739|gb|AK083809|tc|TC1591977 chr11:79387077-79387136 mm|11qB5 PREDICTED: Mus musculus RIKEN cDNA D130012P04 gene (D130012P04Rik), mRNA [XM_003085392] ACAGAGTCATCTTCAGCTACATAATGAGTTCCAGACCTGCCTGGGCTATATTATGAGACT
7 192 316 CUST_144_PI428592664 CUST_144_PI428592664 FALSE TCONS_00040899 unmapped CTGTGTTGAGAGAAAAATCTGTTATTTGTTAAACCTCCTTCCTACAGAGTGGACCCAGAA
8 192 314 A_30_P01020732 lincRNA FALSE chr14:26077008-26277280_R chr14:26261466-26261407 mm|14qA3 lincRNA:chr14:26077008-26277280 reverse strand ATAAGTGACTCACCTTCTCACAAAGAGCAAGAATCACAGAGGTCAGATTGTCTCCTCCTG
9 192 312 A_55_P1987775 A_55_P1987775 FALSE NM_001024137 NM_001024137 78390 Pla2g4d phospholipase A2, group IVD Mm.330507 ENSMUST00000094665 ref|NM_001024137|ens|ENSMUST00000094665|gb|AK019180|gb|AB195276 chr2:120091676-120091617 mm|2qE5 Mus musculus phospholipase A2, group IVD (Pla2g4d), mRNA [NM_001024137] GO:0004620(phospholipase activity)|GO:0004623(phospholipase A2 activity)|GO:0005737(cytoplasm)|GO:0008152(metabolic process)|GO:0009395(phospholipid catabolic process)|GO:0016020(membrane)|GO:0016042(lipid catabolic process)|GO:0016787(hydrolase activity)|GO:0031410(cytoplasmic vesicle)|GO:0046872(metal ion binding) CTGTTCTGTCCCTAGTTTGTTGAGTGGTTTTGTTGTTAGTGATATCATAAAAAGGTATTG
10 192 310 A_51_P215038 A_51_P215038 FALSE NM_182991 NM_182991 67937 Tmem59l transmembrane protein 59-like Mm.23002 ENSMUST00000045286 ref|NM_182991|ens|ENSMUST00000045286|gb|AK005155|gb|BC056172 chr8:73007887-73007828 mm|8qB3.3 Mus musculus transmembrane protein 59-like (Tmem59l), mRNA [NM_182991] GO:0003674(molecular_function)|GO:0005575(cellular_component)|GO:0005794(Golgi apparatus)|GO:0008150(biological_process)|GO:0016020(membrane)|GO:0016021(integral to membrane) CCCTCTGCTAAGGTTCCTTCCCTTTGTCTCTGGAAACCCAACCCCACAAGGACAGAGTGG
11 192 308 A_55_P2101031 A_55_P2101031 FALSE NM_019536 NM_019536 56087 Dnahc10 dynein, axonemal, heavy chain 10 Mm.261014 ENSMUST00000058440 ref|NM_019536|ens|ENSMUST00000058440|ens|ENSMUST00000141137 chr5:125212825-125212884 mm|5qF Mus musculus dynein, axonemal, heavy chain 10 (Dnahc10), mRNA [NM_019536] GO:0000166(nucleotide binding)|GO:0003777(microtubule motor activity)|GO:0005524(ATP binding)|GO:0005858(axonemal dynein complex)|GO:0007018(microtubule-based movement)|GO:0008152(metabolic process) GTTCTTAATGAATCTGCAGAAATTTGAGAACAACATTCAAAGGACTATACAGCAGCTTGA
12 192 306 A_55_P1968315 A_55_P1968315 FALSE XM_003084433 XM_003084433 100038431 Gm10568 predicted gene 10568 Mm.363054 ref|XM_003084433|ref|XM_003086151|gb|AK140060|riken|B230115G11 chr1:3671790-3671849 mm|1qA1 PREDICTED: Mus musculus predicted gene 10568 (Gm10568), mRNA [XM_003084433] CAACACAATCCAGCTGAAACAAAGAATAGATCTGTGTTTTTTCCTAATCAGAGCTGAAAA
13 192 304 A_55_P1964004 A_55_P1964004 FALSE BY456555 Mm.482330 gb|BY456555|tc|TC1675929 chr5:066228933-066228874 mm|5qC3.1 BY456555 RIKEN full-length enriched, adult male thymus Mus musculus cDNA clone K630090P20 3', mRNA sequence [BY456555] GGGGGTCTTAATCTCATTAGTAAAATGATCTAAGAATGGATTCCAATGGAAACTTAAGCT
14 192 302 CUST_274_PI428592655 CUST_274_PI428592655 FALSE TCONS_00306493 unmapped AACAAAAGGAAGCCAGATCTTCTGGATAAGCCTCATGAGTCTTACCTGGAAACTCCCGAA
15 192 300 A_52_P237159 A_52_P237159 FALSE NM_175318 NM_175318 101685 Spty2d1 SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) Mm.155687 ENSMUST00000061639 ref|NM_175318|ens|ENSMUST00000061639|nap|NAP007437-001 chr7:54245985-54245926 mm|7qB4 Mus musculus SPT2, Suppressor of Ty, domain containing 1 (S. cerevisiae) (Spty2d1), mRNA [NM_175318] GO:0003674(molecular_function)|GO:0005575(cellular_component)|GO:0008150(biological_process) GCGTGATTACGAGTGGAATATAGATTTCTCTGGCATTATTAAATCCATGATGTCTTTTAC
16 192 298 A_55_P2104761 A_55_P2104761 FALSE chr7:087382604-087382545 mm|7qD3 AAATGGTGGAAAAGGACCAAGATGGGGGCTATAAGCTAACACCTCAGGAACAAGAGATTG
17 192 296 CUST_174_PI428592655 CUST_174_PI428592655 FALSE TCONS_00211158 unmapped CTGTTGTGAAGTTTCAGGCAGGTGCTGGGAAACAACTTTGGATTATAGAATCTAAACTGC
18 192 294 A_30_P01031549 lincRNA FALSE chr1:95871175-95886625_F chr1:95883705-95883764 mm|1qD lincRNA:chr1:95871175-95886625 forward strand TTCCCTAACTGAATCAATAGAAGCGACTTTCAGTCATGTGGTCTACACACTGTTCTCTAT
19 192 292 A_30_P01029659 lincRNA FALSE chr7:134620707-134626739_F chr7:134622310-134622369 mm|7qF3 lincRNA:chr7:134620707-134626739 forward strand TTTTAAAGGGGTGGTCCTTCCTCTTCCTCTGGGAGACTTGCCTCGACCCCTGGCACGGGG
20 192 290 A_55_P2111825 A_55_P2111825 FALSE NM_029285 NM_029285 75434 1700001C02Rik RIKEN cDNA 1700001C02 gene Mm.332291 ENSMUST00000031078 ref|NM_029285|ens|ENSMUST00000031078|gb|AK005574|gb|BC060996 chr5:30786401-30786460 mm|5qB1 Mus musculus RIKEN cDNA 1700001C02 gene (1700001C02Rik), mRNA [NM_029285] GO:0003674(molecular_function)|GO:0005575(cellular_component)|GO:0008150(biological_process) CCCAGGGAACCTTGGCCTGACCAGGCTGGCTTGCTTGTAATAAAATCTTCAGCCACAACC

Total number of rows: 62976

Table truncated, full table size 30988 Kbytes.




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