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Platform GPL8618

Query DataSets for GPL8618

Status

Public on Jun 30, 2009

Title

ViaLactia Biosciences custom bovine array 22k version 1b

Technology type

in situ oligonucleotide

Distribution

custom-commercial

Organism

Manufacturer

Agilent Technologies

Manufacture protocol

325,000 EST, mRNA, and CDS region sequences for Bos taurus genes were retrieved from GenBank, and supplemented with paired 5'- and 3'-reads from 100,000 ESTs obtained from normalized bovine fetal brain, lactating and non-lactating mammary gland cDNA libraries. After repeat masking, sequences were clustered by pairwise-comparison using Paracel Transcript Assembler (Paracel, Pasadena, CA, USA) to reduce redundancy, and the resulting clusters were mapped to genes predicted from the 2.1 assembly of the bovine genome. Gene-specific cluster sequences were then supplemented with novel transcript sequences predicted by the NCBI RefSeq project (http://www.ncbi.nlm.nih.gov/RefSeq/). Probe sequences (60-mer) targeted towards the 3' regions of the transcripts were designed by Agilent Technologies. 21,495 unique probe sequences were selected for array manufacture by in-situ synthesis.

Support

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Description

This array is an early version of the now commercially available Agilent Bos taurus 44k array (Agilent design ID 015354).

Contributor(s)

Lehnert K, Ward H

Submission date

May 31, 2009

Last update date

Jun 30, 2009

Contact name

Matt D Littlejohn

E-mail(s)

matt.littlejohn@vialactia.com

Phone

+64 9 589 4572

Fax

+64 9 525 1096

Organization name

DairyNZ

Street address

PO Box 109-185 Newmarket

City

Auckland

ZIP/Postal code

1061

Country

New Zealand

Samples (12)

More...

GSM419915, GSM419916, GSM419917, GSM419918, GSM419919, GSM419920

Series (1)

Analysis of milk removal frequency on bovine mammary gene expression

Data table header descriptions
ID
GB_ACC	GenBank Accession number
SEQUENCE	60mer probe sequence
SPOT_ID

Data table
ID	GB_ACC	SEQUENCE	SPOT_ID
(-)3xSLv1		GCTAGCGAAAGCTAGCTTTTCGATCGGAAACGATCGTTTTCCAGTGACGAAAGTCACTGG	CONTROL
(-)GD11		GCTAGCTAGCTAGCTAGCGCTAGCGAAAGCTAGCGCTAGCTAGCTAGCTAGCTTTTTTTT	CONTROL
(+)Pro25G_onG3PDH570_10Ts		ATCATCGTAGCTGGTCAGTGTATCCGTGTGAACCATGAGAAGTATGACAATTTTTTTTTT	CONTROL
0.CB1_2321	XM_877554	CACACCTGGGTTCAAATTCTAGCTCCAGTATATGACTGGCTATGGGGACTTTGGTAAGAT
1.C104_1884	NM_001035369	AAACACAAGAGTCTGAATGTATGTTAATCCGTAATCCCTGGCTGATTATCCCTGTGTTAC
1.C114_1817	XM_581318	GAGAAAACTTTTCTTCCTGGCAGATAGCTTAAAGAGTGGGGTATATAAAATCACAAAATG
1.C117_818	XM_583669	TATGTCCCAAGATGGATTCCCAAATGAAGATGGAGAACAAATGACCCCTGAGCTTCTGCT
1.C120_537	XM_582744	TGAAGAAGGGTCCTCCAGTAGCCCCCAAGCCAGCCTGGTTTCGCCAAAGCTTGAAAGGTT
1.C123_1514	XM_001253337	GGAGCGGAAGGCAGAAGGGGTGTGATTGAAGTGTGTCCAGAGATGAAAAAATACATATAT
1.C124_2002	NM_182786	CCTTGAGGTCTTTTGACATGTGGAAAGTGAACTTGAATGAAAAATTTAAGCATTGTTTGC
1.C130_1274	XM_865974	AGGCAGTGAAGATGTTGGGGGCCACTTTTCAGTCAACTTCCTTTTCCCAATAAAAGCCTT
1.C135_880	BM445350	TTTTTCCCCAAATATTTGTGCTTTAGATGTAGTTACCAGATGAATTTTCCACGTATGCTC
1.C136_589	NM_001034433	TGTAGGGGGCAGCCCCAGCCCTGACCTGGGCTTACTGTCACATAGCTCTGACTTTTTGTT
1.C139_2175	XM_591717	TCTGACTTGTGACCTGGACTCAACAACCTTGGGGTGTGTTTCTCCATAAAGCAGTTTTGA
1.C142_549	NM_001001175	CAGACCTGGCCCACCCCAATGTGCTGGCCTTCCAATAAAGCTGGATGAGAAACCGCCAAA
1.C143_1467	XM_614481	GAAGACAGGGAACGTGACTGAAATGTATTTATCGGGTTTTTGTTTAGTTCAATAGCTTGT
1.C144_414	NM_001015512	GACAAAGACCGCAAAAAGATCCTCGAACGTAAAGCCAAATCTCGCCAAGTAGGAAAGGAA
1.C145_1085	NM_205794	GACTGTGACATTTATTTTCCAAAGTTTCTAAAGAATACGGGTCTGTGGTGATAAATACAG
1.C150_569	XM_878295	TCCATTGCTTACCAGCTTTCTATTCTGTAACACAAAACTATCCTAATCTTTGAATGTGAG
1.C153_869	NM_001015543	TTGTCTGGATCCGCCAGCCCAGGAGGTGCTGTGTGTTCCTGTTACTATTAAAATACTATT

Total number of rows: 21844

Table truncated, full table size 1814 Kbytes.

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

Supplementary data files not provided

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