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Platform GPL6049 Query DataSets for GPL6049
Status Public on Oct 26, 2007
Title Arizona Gallus gallus 20.7K Oligo Array v1.0
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Gallus gallus
Manufacturer Genomics Research Laboratory, Steele Children's Research Center, University of Arizona
Manufacture protocol 1. Oligo Design.
The chicken oligos were designed by Carre et al. (2007) using gene predictions from Ensembl, TIGR, full-length cDNAs from the BBSRC UMIST ChickEST database, and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned and 70mer oligos designed against regions common to more than one aligned sequence. Oligos were then designed using OligoArray2.0.
2. Oligo Array Manufacturer.
The chicken oligo set [Gallus gallus (chicken) Roslin/ARK CoRe Array V1.0] was manufactured by Operon Technologies, Inc.. The chicken oligo set (Catalog # 851102) contains 20,460 long oligo probes (300 pmol) arrayed in 54 384-well plates. Four wells in each of the 54 384-well plates contained the Operon Production Tracking Oligo opHsV04NC000001, which is a randomly-generated oligo sequence with a length of 30 bases.
3. Printing.
This 20.7K chicken oligo array contains 20,676 features that include 20,460 70mer oligos and 216 control spots of the Operon Production Tracking Oligo opHsV04NC000001. The oligos (300pmol) were dissolved in 8 microliters of 50% DMSO for printing. The chicken oligo array was printed on Corning® UltraGAPSTM aminosilane coated slides (Cat # 40018) using a Virtek ChipWriter Pro (Model # HCO1-M) robot fitted with 48 TeleChem (SMP2.5) pins. The slides were printed in a HEPA-filtered positive-pressure chamber maintained at 24 degrees C and 48% relative humidity (RH)(± 2 %RH). The printed slides were dried overnight at room temperature (22-25 degrees C with 20-40 %RH). The slides were then stored in a chemical (Drierite) desiccator at room temperature until use.
Support glass
Coating aminosilane
 
 
Web link http://www.grl.steelecenter.arizona.edu/index.asp
Contributor(s) Trakooljul N, Konieczka JH, Hoying A, Antin PB, Porter TE, Cogburn LA
Submission date Oct 23, 2007
Last update date Jan 18, 2013
Contact name Larry Albert Cogburn
E-mail(s) cogburn@udel.edu
Phone 302-831-1335
Organization name University of Delaware
Department Animal and Food Sciences
Lab Avian Functional Genomics
Street address 531 South College Ave.
City Newark
State/province DE
ZIP/Postal code 19717
Country USA
 
Samples (220) GSM244284, GSM244285, GSM244286, GSM244287, GSM244288, GSM244289 
Series (6)
GSE9745 Hepatic Transcriptional Profiling of Hatchling Chicks and Market-age Broiler Chickens during Fasting and Re-feeding
GSE13257 Analysis of Genes in the Hypothalamus Controlling Feed Intake and Energy Metabolism in Neonatal Chicks
GSE16653 Functional Study of the Chicken microRNAs miR-143 and miR-10a

Data table header descriptions
ID
MetaColumn Array coordinate information
MetaRow Array coordinate information
Block Array coordinate information
Row Array coordinate information
Column Array coordinate information
OLIGO_ID Roslin Institute Gallus Gallus (RIGG) Oligo Identifier (ID)
Reporter_Type Oligo (PROBE) or Control (CONTROL) or Blank (BLANK) Spot
GI NCBI Gene Identification Number (GI)
GB_ACC GenBank Accession number
GenBank_Definition GenBank Definition
Entrez_GeneID NCBI Entrez Gene Identifier
Entrez_Symbol NCBI Entrez Gene Symbol
Entrez_Description NCBI Entrez Gene Description
Other_Aliases Other Gene Symbol
Ensembl_ID Ensembl Gene Identifier
Ensembl_Symbol Ensembl Gene Symbol
Ensembl_Description Ensembl Gene Description
SEQUENCE Probe sequence
Spot_number Spot reference number

Data table
ID MetaColumn MetaRow Block Row Column OLIGO_ID Reporter_Type GI GB_ACC GenBank_Definition Entrez_GeneID Entrez_Symbol Entrez_Description Other_Aliases Ensembl_ID Ensembl_Symbol Ensembl_Description SEQUENCE Spot_number
1 1 1 1 1 1 RIGG19870 PROBE 118129332 XM_428163 "PREDICTED: Gallus gallus hypothetical LOC430608 (LOC430608), partial mRNA" 430608 LOC430608 hypothetical LOC430608 ENSGALG00000008427 GNAT2 GCTGCACTCAGTGCCTATGACATGGTTCTGGTGGAAGATAAAGAAGTGAACAGAATGCATGAAAGCCTTC 1.1.1
2 1 1 1 1 2 RIGG18766 PROBE 118088834 XM_419852 "PREDICTED: Gallus gallus zinc finger protein 292 (ZNF292), mRNA" 421828 ZNF292 zinc finger protein 292 ENSGALG00000015823 ZNF292 AGACAGATCACGGTGTTAAGATAAGGCCAAACAAGGTAGAAGATGATGGTGTATTCAAGTGTGACTGTGAGGGC 1.1.2
3 1 1 1 1 3 RIGG17661 PROBE 118087235 XM_418360 "PREDICTED: Gallus gallus similar to infertility-related sperm protein (LOC420249), mRNA" 420249 SPAG1 sperm associated antigen 1 ENSGALG00000016037 SPAG1 ATGGAGCGGTATCGACAGGCATATGTTGATTACAAAACAGTCCTACAAATAGACAGCAGCATACAAGCAG 1.1.3
4 1 1 1 1 4 RIGG16838 PROBE 41633484 BX932956 "Gallus gallus finished cDNA, clone ChEST915l7" 423588 GNPNAT1 glucosamine-phosphate N-acetyltransferase 1 ENSGALG00000012414 GNPNAT1 AAGAAATCTGGAGATTACTACGTTACTGTCGTAGAAGACACGAATCTTGGACAGATCGTTGCTACAGCAA 1.1.4
5 1 1 1 1 5 RIGG15734 PROBE ENSGALG00000010521 COL25A1 TCCAGAAATCTTCGCCTATATGAGCAGAGAAATGGATGTCAGTGAAGTAACTCAGATGTGCTACATGTGA 1.1.5
6 1 1 1 1 6 RIGG14629 PROBE 118085741 XM_418619 "PREDICTED: Gallus gallus signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 (STAM), mRNA" 420517 STAM signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 ENSGALG00000008654 STAM TGCTGCTTATCAGAATGCTGGAACTAATATGTCCCAGGTGCCAAACTATAACTTAGCATCTACACCTCTG 1.1.6
7 1 1 1 1 7 RIGG13525 PROBE 118094854 XM_422590 "PREDICTED: Gallus gallus glypican 1 (GPC1), mRNA" 424770 GPC1 glypican 1 ENSGALG00000002342 GPC1_CHICK Glypican-1 precursor (Heparan sulfate proteoglycan core protein). [Source:Uniprot/SWISSPROT;Acc:P50593] GTGAGATGGAGGAGAACTTTGCAAACAAAAGCAGAAGTGAATTCGAAGCCATGATGAAAGAGGCGGGCCG 1.1.7
8 1 1 1 1 8 RIGG12702 PROBE 53136785 AJ721063 "Gallus gallus mRNA for hypothetical protein, clone 33o1" 422021 RCJMB04_33o1 elongation protein 3 homolog (S. cerevisiae) "RCJMB04_33o1, ELP3" GTCTGTACTGAAGCAGTTGGGTCACAGCGTGGATAAAGTGGAGTTCGTTGTGATGGGTGGAACTTTCACG 1.1.8
9 1 1 1 1 9 RIGG11598 PROBE 118095608 XM_413750 "PREDICTED: Gallus gallus similar to mKIAA1055 protein (LOC415364), mRNA" 415364 TBC1D2B "TBC1 domain family, member 2B" ENSGALG00000003322 TBC1D2B GAGGACCTATCACCTGGAGAAAGTGCGTCTGGAGCTCAATGAACTTGAAGCCATTCGTGAGGATTTCCTG 1.1.9
10 1 1 1 1 10 RIGG10494 PROBE 118098354 XM_415062 "PREDICTED: Gallus gallus similar to Phosphatidylinositol 4-kinase, catalytic, alpha polypeptide (LOC416767), mRNA" 416767 PI4KA "phosphatidylinositol 4-kinase, catalytic, alpha" PIK4CA ENSGALG00000001386 Phosphatidylinositol 4-kinase alpha (EC 2.7.1.67) (PI4-kinase) (PtdIns-4-kinase) (PI4K-alpha). [Source:Uniprot/SWISSPROT;Acc:P42356] [from human gene ENSG00000133511] ACAGACTTTGGGATGTACGATTACTTTACAAGGCAATACGGTGATGAGTCTACTCTTGCATTCCAGAAGGC 1.1.10
11 1 1 1 1 11 RIGG09389 PROBE 118103943 XM_001232743 "PREDICTED: Gallus gallus similar to FCH domain only 2 (LOC769464), mRNA" 769464 FCHO2 FCH domain only 2 ENSGALG00000015019 FCHO2 GCCACTTGGATCTTGTGCGGAGATTACAAGAGCTGATAAAAGAAGTTCACAAGTATGGAGACGAACAAATT 1.1.11
12 1 1 1 1 12 RIGG08566 PROBE 118082085 XM_415951 "PREDICTED: Gallus gallus similar to p120-PI3K (LOC417706), mRNA" 417706 PIK3CG "phosphoinositide-3-kinase, catalytic, gamma polypeptide" ENSGALG00000008081 PIK3CG GAAGTGAGATTGCCCAGTCTATGCACTACCAACAGAGGTTCGCTGTGATCCTAGAAGCCTATCTTCGGGG 1.1.12
13 1 1 1 1 13 RIGG07462 PROBE 47022824 CR407290 "Gallus gallus finished cDNA, clone ChEST605a1" 421492 HNRNPU heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) HNRPU ENSGALG00000010671 Q2MHD2_CHICK Scaffold attachment factor A (Fragment). [Source:Uniprot/SPTREMBL;Acc:Q2MHD2] CAGGGTCAATTCTGGGGTCAGAAGCCATGGAGTCAGCATTATCACCAAGGATATTATTGAATACCCAAATA 1.1.13
14 1 1 1 1 14 RIGG06358 PROBE 118101017 XM_001234040 "PREDICTED: Gallus gallus similar to Gamma-aminobutyric acid (GABA) A receptor, delta (LOC770710), mRNA" 770710 GABRD "gamma-aminobutyric acid (GABA) A receptor, delta" ENSGALG00000001282 GABRD CAGGAATGCATGTTGGACTTGGAGAGCTATGGTTACTCTTCAGAGGACATTGTCTACCACTGGTCAGAAA 1.1.14
15 1 1 1 1 15 RIGG05253 PROBE 118090463 XM_420686 "PREDICTED: Gallus gallus similar to Myotubularin-related protein 7 (LOC422731), mRNA" 422731 MTMR7 myotubularin related protein 7 ENSGALG00000013646 VPS37A GCAGTCTGCTGTGATGCGTCTTTGAATCCTTGGAATTTTGCATTACTTACTATTGTTTTCACTGCAGTGT 1.1.15
16 1 1 1 1 16 RIGG04430 PROBE 46429399 CR390754 "Gallus gallus finished cDNA, clone ChEST628h10" 416615 LOC416615 similar to MGC64341 protein ENSGALG00000006916 GDE1_HUMAN TTGCAGATCCCCTCTAGCTACCCTTCTGTCCGATTTGGTGAAATGCAGTCCAGAGAAGTTATGAGAAAGTCTCAT 1.1.16
17 1 1 1 1 17 RIGG03326 PROBE 41633301 BX932773 "Gallus gallus finished cDNA, clone ChEST481h6" 415422 TMOD2 tropomodulin 2 (neuronal) ENSGALG00000004740 TMOD2 TATGACCTTGCAGCTGTTCTTGGAGTGCACAACATGGTCAACAACCCAAAATTTGATGAAGGAGGAGCCC 1.1.17
18 1 1 1 1 18 RIGG02221 PROBE 48842061 CR523399 "Gallus gallus finished cDNA, clone ChEST309i19" ENSGALG00000000541 ZC11A_CHICK Zinc finger CCCH domain-containing protein 11A. [Source:Uniprot/SWISSPROT;Acc:Q5ZJJ1] TACGGTCCGAGAAGAGAACCAATTCCTTACAAAACCAAAATCAATTGAAGATGCTCGGTACCGTGCAGCC 1.1.18
19 1 1 1 1 19 RIGG01118 PROBE 45425511 CR353821 "Gallus gallus finished cDNA, clone ChEST151e14" CCTCAAGAAGTACTTCGACAGCTGCAATGGGGATCTGGACCCTGAGATCGTGAAGTCCTTCATGTACCAG 1.1.19
20 1 1 1 1 20 RIGG00294 PROBE 53135039 AJ720730 "Gallus gallus partial mRNA for hypothetical protein, clone 24e12" 396017 RCJMB04_24e12 "enolase 1, (alpha)" "RCJMB04_24e12, ENO1" ENSGALG00000002377 ENOA_CHICK Alpha-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Non- neural enolase) (NNE) (Enolase 1) (Phosphopyruvate hydratase) (C-myc promoter-binding protein) (MBP-1) (MPB-1) (Plasminogen-binding protein). [Source:Uniprot/SWISSPROT;Acc:P06733] [from human gene ENSG00000074800] CCTCAACTGGAATCTATGAAGCTCTAGAACTTCGTGACAATGACAAGACACGCTACTTGGGAAAAGGTGT 1.1.20

Total number of rows: 21120

Table truncated, full table size 5602 Kbytes.




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