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Platform GPL13191 Query DataSets for GPL13191
Status Public on Feb 20, 2011
Title Arizona Gallus gallus 20.7K Oligo Array v1.5
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.
 
 
Submission date Feb 18, 2011
Last update date Feb 20, 2011
Contact name Parker B Antin
E-mail(s) [email protected]
Phone 52062606382
Fax 5206267600
Organization name University of Arizona
Department Cell Biology and Anatomy
Street address 1656 E. Mabel Street
City Tucson
State/province AZ
ZIP/Postal code 85724
Country USA
 
Samples (4) GSM677699, GSM677700, GSM677701, GSM677702
Series (1)
GSE27403 Gallus gallus Control Versus SU5402, LY294002 or U0126 Treated Preingression Epiblast from Gastrula Stage Embryos

Data table header descriptions
ID
Meta row
Meta col
Row
Col
Probe ID
Entrez gene ID
Entrez gene description
Ensembl gene ID
Ensembl gene description
GENE
SPOT_ID
SEQUENCE

Data table
ID Meta row Meta col Row Col Probe ID Entrez gene ID Entrez gene description Ensembl gene ID Ensembl gene description GENE SPOT_ID SEQUENCE
1.1.1.1 1 1 1 1 NA --unknown
1.1.1.2 1 1 1 2 RIGG00006 NA --unknown CCTTGAAGAAAGGGAAAATGAAGATAGCATGGTGCCACTTCCGAAGCAAAGCCTGAAGTTCTTCTGTGCT
1.1.1.3 1 1 1 3 RIGG00024 431122 nucleoporin 160kDa ENSGALG00000000453 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5ZMT2] 431122 GATTGAAACGAGTTTGAATTGGCCCCATCTCATTACCGCAATAGTGGCTGACTTTCTGCCCCTCCTATGG
1.1.1.4 1 1 1 4 RIGG00030 424600 nuclear autoantigenic sperm protein (histone-binding) ENSGALG00000010255 Nuclear autoantigenic sperm protein (NASP). [Source:Uniprot/SWISSPROT;Acc:P49321] [from human gene ENSG00000132780] 424600 GGGCTGCAGTTGAAAGCACAGTATGATAATTCTTTAGCTTTGGACACTCCTCTCCTTCAAAGGAAAATGG
1.1.1.5 1 1 1 5 RIGG00047 395414 "chaperonin containing TCP1, subunit 4 (delta)" ENSGALG00000008812 "chaperonin containing TCP1, subunit 4 (delta) [Source:RefSeq_peptide;Acc:NP_996761]" 395414 CCACCATCATCTCAGAGTCATTCCAGAAAGCTTTAGAGAAAGGTATTGAAGTATTGACCAACATGGCACAG
1.1.1.6 1 1 1 6 RIGG00053 416206 similar to Adult retina protein ENSGALG00000002878 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5ZMD5] 416206 TCTTGGCAAGCAGTTCAGATCCAGACTTCATGTATGAACTGGACAGAGAAATGGACTACCAGCAAAGCTC
1.1.1.7 1 1 1 7 RIGG00071 416708 ectonucleoside triphosphate diphosphohydrolase 6 (putative function) ENSGALG00000008563 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5ZM23] 416708 CTTGACTGTACAGCATCTGTTGTCAACTTCCTGTAAAACTTGATCATCATTGAAGGAGAACCAGCACTCTG
1.1.1.8 1 1 1 8 RIGG00077 418702 thioredoxin domain containing 9 ENSGALG00000016763 Hypothetical protein (Fragment). [Source:Uniprot/SPTREMBL;Acc:Q5ZLZ7] 418702 AATGGAGATTAGGCTGTGCAGATATAATTAATTACAGTGGGAAACTTGATGGACCACCTTTTCAAAGCCC
1.1.1.9 1 1 1 9 NA --unknown
1.1.1.10 1 1 1 10 RIGG00382 424439 ring finger and CCCH-type zinc finger domains 1 ENSGALG00000004587 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5F439] 424439 CACCCATGTTCTCCATATCTTCACGCATATTTACTTTGCTCTTAGTTGAGCTTCAGCCTCTTAACTGCTA
1.1.1.11 1 1 1 11 RIGG00400 421138 thymocyte selection-associated high mobility group box ENSGALG00000015448 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5F3T5] 421138 TGGTTCTCCATCATCTCAATGTCAGATGACCTCTTTTAGTTTATATCAGCTAAATGCCCGGCTTTACCTGT
1.1.1.12 1 1 1 12 RIGG00406 417198 nucleoporin 188kDa ENSGALG00000004548 Hypothetical protein. [Source:Uniprot/SPTREMBL;Acc:Q5F3Q0] 417198 CGATCAGTCACTGGACCTTGCTGAGTACAACGTGCTCTTTGTCTTGAGTTTCACCACACCAGCCTTTGAT
1.1.1.13 1 1 1 13 RIGG00424 424671 "myb-like, SWIRM and MPN domains 1" ENSGALG00000010869 "Protein MYSM1 (Myb-like, SWIRM and MPN domain-containing protein 1). [Source:Uniprot/SWISSPROT;Acc:Q5F3F2]" 424671 ACTGCGGTGATGTTAACTGTATTGGACGGATCCACACGTACTTGGAATTAATAGGAGCAATTAACTTCGG
1.1.1.14 1 1 1 14 RIGG00430 NA --unknown GCTGTTGGTGCAAATGGGATATTTCATTGAGGAGAACGGTTTTGAACTTACGTGAAGAGCATGGAATTGT
1.1.1.15 1 1 1 15 RIGG00448 428697 bone morphogenetic protein 15 ENSGALG00000004742 Bone morphogenetic protein 15 proprotein. [Source:Uniprot/SPTREMBL;Acc:Q5XX12] 428697 GCTGTCACCTGCACCCATAGGACTCAGTCACACGCACCCCAAGCCATCTCATCCCTGGGTATTTT
1.1.1.16 1 1 1 16 RIGG00454 427406 similar to Small inducible cytokine A19 precursor (CCL19) (Macrophage inflammatory protein 3 beta) (MIP-3-beta) (EBI1-ligand chemokine) (ELC) (Beta chemokine exodus-3) (CK beta-11) 427406 GCAGCGGCTGCACGTTCTCTGCCTTAGTCTCCTGGTGCTGAGATGTGTCCTGCATGTGTATGCTG
1.1.1.17 1 1 1 17 NA --unknown
1.1.1.18 1 1 1 18 RIGG00758 769745 ATP/GTP binding protein-like 3 ENSGALG00000011727 769745 GCTATCTGTACAAAGGCCTAGCAGTCATAGACCTATTTCTAGCATCTCTCAGTGACAGTGAGTTTGCAATC
1.1.1.19 1 1 1 19 RIGG00776 NA --unknown TGCATGAAAAGAGAGAGGGTTGGGGTTTTCTGTTTTATTCGTACTGTACCACACATATTTTCCCCACCCAC
1.1.1.20 1 1 1 20 RIGG00782 427159 serologically defined colon cancer antigen 10 ENSGALG00000014747 427159 GCTAATGAAGAGAGCTATTTGAGTGAGGAGGAAGATGAAAATGACGAAGATGTTGACAGTGTAGAAGGCGAAG

Total number of rows: 21120

Table truncated, full table size 3660 Kbytes.




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