NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL5480 Query DataSets for GPL5480
Status Public on Jul 11, 2007
Title ARK-Genomics G. gallus 20K v1.0
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Gallus gallus
Manufacturer ARK-Genomics, Roslin Institute, Roslin, Midlothian, EH25 9PS, United Kingdom
Manufacture protocol Oligos were resuspended in Corning Pronto Epoxide spotting solution to
give a final concentration of 20uM. DNA was printed on Corning Epoxide
slides using a Genomic Solutions MicroGrid II arrayer and the MicroSpot
10K pins, according to manufacturer's instructions. All printing was
carried out in conditions of constant humidity (52% RH) and temperature
(20C) in a room supplied with HEPA filtered air. Prior to printing the
pins were cleaned by ultra-sonication in water and if necessary 50mM
potassium hydroxide. A test print of all pins was carried out by
printing Cy3 streptavidin conjugate dye in printing buffer onto epoxide
slides and printing 100 features per pin. When all pins were printing
consistent size spots for more than 80 features they were accepted as
ready to print. The MicroGrid II was then programmed for the array print
run, with a grid layout file prepared to allow duplicate printing at
random within a patch. At the end of the print run the slides were
removed following the program instructions in preparation for post
processing.
Slides dessicated overnight and then transferred to a humid chamber (45%
humidity, 42C) for 8 hours. The slides were then washed in 0.2% SDS
(room temperature) for 2 minutes with agitation before being rinsed in
three water washes (30seconds, 30 seconds, 1 minute) with agitation.
After these steps the slides were then incubated in water at 50C for 20
minutes before spin drying. The slides were then stored in a desiccator
in the dark ready for use.
Support glass
Coating other
 
Description This is an oligo array containing 20460 elements. Oligos were designed using gene predictions from Ensembl and TIGR, together with full-length cDNAs from the BBSRC UMIST ChickEST database (http://chick.umist.ac.uk/) and chicken bursal EST sequences from Jean-Marie Buerstedde's DT40 database. Sequences from these resources were aligned together and oligos were designed against regions in common to more than one dataset. Oligos were then designed using OligoArray2.0.
 
Contributor(s) Carre W, Talbot R, Law A, Fell M, Young J, Kaiser P
Submission date Jul 10, 2007
Last update date Jul 11, 2007
Contact name Mark Fell
E-mail(s) mark.fell@bbsrc.ac.uk
Organization name ARK-Genomics@Roslin Institute
Department Bioinformatics
Street address Roslin Institute
City Roslin
State/province Midlothian
ZIP/Postal code EH25 9PS
Country United Kingdom
 
Samples (405) GSM262297, GSM262298, GSM262299, GSM262300, GSM262301, GSM262302 
Series (7)
GSE10380 Analysis of severe feather pecking behavior in a high feather pecking selection line
GSE11290 Transcriptome profiling of feeding-to-fasting transition in chicken liver using a chicken 20K oligo microarray
GSE12319 Chicken family BC1 1940: transcriptome profiling used for QTL/eQTL detection

Data table header descriptions
ID
MetaColumn array coordinate information
MetaRow array coordinate information
Block array coordinate information
Column array coordinate information
Row array coordinate information
Reporter Identifier Oligo identifier
Reporter Name Accession of target sequence
GB_ACC GenBank identifier and Reporter BioSequence DatabaseEntry [embl]
Reporter BioSequence DatabaseEntry [ens_trscrpt_id] Ensembl Transcript ID
Reporter BioSequence DatabaseEntry [ensembl:30] Ensembl:30 Gene ID
Reporter BioSequence DatabaseEntry [mirna] microRNA registry accession: http://microrna.sanger.ac.uk/sequences/
Reporter BioSequence Type type of molecule: ss oligo
Reporter BioSequence Polymer Type type of polymer: DNA
SEQUENCE Reporter BioSequence [Actual Sequence]
Reporter Group [role] Control or Experimental
Reporter Control Type Type of control if control feature
Reporter Comment Reporter Comment
SPOT_ID spot identifier

Data table
ID MetaColumn MetaRow Block Column Row Reporter Identifier Reporter Name GB_ACC Reporter BioSequence DatabaseEntry [ens_trscrpt_id] Reporter BioSequence DatabaseEntry [ensembl:30] Reporter BioSequence DatabaseEntry [mirna] Reporter BioSequence Type Reporter BioSequence Polymer Type SEQUENCE Reporter Group [role] Reporter Control Type Reporter Comment SPOT_ID
1 1 1 1 1 1 RIGG14714 ENSGALT00000014280 ENSGALT00000014280 ENSGALG00000008782 ss_oligo DNA ATGTTTGTGATGGGTGTCAACCATGAGAAATATGACAAGTCCCTGAAAATTGTCAGCAATGCATCGTGCA Control control_biosequence GAPDH cntrl --Control: GAPDH cntrl
2 1 1 1 1 2 RIGG01251 ChEST175g3 CR352486.1 ss_oligo DNA TAATACACATCAAGCTATATGCAGGTGACACTCCTAAGTTGCCAACAACATGAAGATAGGGCTGTGTGTG Experimental Similar to CYPB_MOUSE (P24369) Peptidyl-prolyl cis-trans isomerase B p
3 1 1 1 1 3 RIGG15162 ENSGALT00000015537 ENSGALT00000015537 ENSGALG00000009547 ss_oligo DNA TTCTCTGAGACAGGAACGTAGCGAACAGGGCTCACTATGGACCAGACAGTCTTCAGGTGGTAGATCTGAG Experimental ENSGALT00000015537.1 ENSGALT00000015537
4 1 1 1 1 4 RIGG17066 ENSGALT00000020887 ENSGALT00000020887 ENSGALG00000012803 ss_oligo DNA GAACTGTGCCCAAGAGTCCCAAGAAATCACGGCCTCTACAAAATCACGCCCTGTTACATAGACAACCCTG Experimental ENSGALT00000020887.1 ENSGALT00000020887
5 1 1 1 1 5 RIGG06544 ChEST910e20 CR524258.1 ENSGALG00000005604 ss_oligo DNA TCCAGTTGAGACCATACTTCTACAGCAGCAATGGGTGAAGCGATCAAACAAAGGTTTCAGGGGCTCCTTT Experimental Genome Hit Contig66.38
6 1 1 1 1 6 RIGG08747 ENSGALG00000009602 ENSGALG00000009602 ss_oligo DNA TCAGCTTGGAGAGGATATGAAGCTCGCAGGAAGTACAAGGAAATAAGGAACAGAAGAAATAATGCTGCTATA Experimental ENSGALG00000009602.1-2 ENSGALG00000009602
7 1 1 1 1 7 RIGG10299 ENSGALT00000001525 ENSGALT00000001525 ENSGALG00000001029 ss_oligo DNA AGCAGAGTCCTGAGCCTCTGTATTTTGAGGATGAAGATGAGTTTCCAGAACTAAATAGTGACAATGGCAAC Experimental ENSGALT00000001525.1 ENSGALT00000001525
8 1 1 1 1 8 RIGG14411 ENSGALT00000013469 ENSGALT00000013469 ENSGALG00000008276 ss_oligo DNA CGAGTCCATTGTGTCCTGGGACATCAAGGAGTGGTCTTCATTGTTTTACATGTACTAAAGCAGTTTCTTA Experimental ENSGALT00000013469.1 ENSGALT00000013469
9 1 1 1 1 9 RIGG03530 ChEST50c3 CR387648.1 ss_oligo DNA CAAGGAGGACTTAATGATCTTACGGGTCTCCTGCAACTGAAACAACTCTATAACTCTGTGACTTCCCAGC Experimental Genome Hit Contig19.530
10 1 1 1 1 10 RIGG18970 ENSGALT00000026029 ENSGALT00000026029 ENSGALG00000016156 ss_oligo DNA AAGCCTGTACCCAGTGCAGTTTTACCTGTGACATCTTTGGAGACTTCAACTTATATTTCCTCCTTTGTTTC Experimental ENSGALT00000026029.1 ENSGALT00000026029
11 1 1 1 1 11 RIGG05792 ChEST801g18 CR407182.1 ENSGALG00000014961 ss_oligo DNA TTCACAGGCTAGTTGAAGAAGGCCAGAAAGAAATCAATGAGGAAAGAGAGACAACATATGACTTCGTAGACAGAA Experimental Similar to Q8C3G8 (Q8C3G8) Hypothetical protein
12 1 1 1 1 12 opHsV04NC000001 opHsV04NC000001 ss_oligo DNA Control control_biosequence operon QC control --Control: operon QC control
13 1 1 1 1 13 RIGG08018 ENSGALG00000003759 ENSGALG00000003759 ss_oligo DNA TCTCCAGATCAGTCGGGTCTTGATATTAATGGAATCAAACCAGAACCAATATGTGACTACACACCAGCAT Experimental ENSGALG00000003759.1 ENSGALG00000003759
14 1 1 1 1 14 RIGG04282 ChEST608d24 CR523265.1 ss_oligo DNA TGTGTCCCTGAACCAAACATGATTACTGAGTTAGTGGTTGTTGGTTATGTTATGTGTTACACTGAGTGGCA Experimental Genome Hit Contig98.83
15 1 1 1 1 15 RIGG17048 ENSGALT00000020839 ENSGALT00000020839 ENSGALG00000012771 ss_oligo DNA TACATCTGGACTTGTCCTTCTAAAACCAATTAGATTGCTGAAACAATGGGACACAAGTTGGACGAGATGA Experimental ENSGALT00000020839.1 ENSGALT00000020839
16 1 1 1 1 16 RIGG02761 ChEST385i7 BX934616.2 ENSGALG00000011047 ss_oligo DNA TGTTGTGGTTAAATAACCCCTTTTCAACTAGCACCCGCGTTTCCATAAAGATGACTGAAATCAGCGCTCC Experimental Weakly similar to OBRG_RAT (Q9JLS8) Leptin receptor gene-related protein (OB-
17 1 1 1 1 17 RIGG19304 ENSGALT00000026992 ENSGALT00000026992 ENSGALG00000016727 ss_oligo DNA ATCACGAAGGTTTCTCACATTCCACCAAGTCGATGGGCTTTAGTGTGTAGTTTATGCAAACTGAAAACCG Experimental ENSGALT00000026992.1 ENSGALT00000026992
18 1 1 1 1 18 RIGG14387 ENSGALT00000013404 ENSGALT00000013404 ENSGALG00000008237 ss_oligo DNA GGATTTCAATGAAGACTATTCTGATCTCGATGGAATAGTACAGGAGCAGAGACAAGAGATGGAGGAGTCCA Experimental ENSGALT00000013404.1 ENSGALT00000013404
19 1 1 1 1 19 RIGG04664 ChEST658j11 CR406578.1 ss_oligo DNA AAGGCCATCATCCACGTGTCAGCCGCGCTCTTCACCCTCCACAATAAGAACATCGAGACCCACCT Experimental Similar to NCP1_HUMAN (Q9Y2A7) Nck-associated protein 1 (NAP 1) (p125N
20 1 1 1 1 20 RIGG06144 ChEST852g11 BX934664.1 ss_oligo DNA CCTTTCAAAGGAGGAACGCTTCAGATGGGTACAAATCTGAGTTTACTGTCTCCTGGTTTGTGGGTTAGAAAGTGT Experimental Weakly similar to AAH53822 (AAH53822) Hypothetical protein

Total number of rows: 22176

Table truncated, full table size 4594 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp

Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap