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Platform GPL1796

Query DataSets for GPL1796

Status

Public on Jan 17, 2005

Title

Chlamy 36mer array

Technology type

spotted oligonucleotide

Distribution

non-commercial

Organism

Chlamydomonas reinhardtii

Description

389,285 different 36-mer oligonucleotide probes were selected from the V2 genome sequence of Chlamydomonas reinhardtii that was available from the JGI website (ftp://ftp.jgi-psf.org/pub/JGI_data/Chlamy/chlre2/) in February 2004. The probes are covering predicted proteins and intergenic regions. The selected oligonucleotides were synthesized on a glass-based array using an in situ maskless photolithographic synthesis device.

Contributor(s)

Stolc V, Samanta MP, Tongprasit W, Marshall WF

Submission date

Jan 14, 2005

Last update date

May 26, 2005

Contact name

Waraporn Tongprasit

E-mail(s)

wtongprasit@mail.arc.nasa.gov

Phone

1-650-604-4779

URL

http://phenomorph.arc.nasa.gov

Organization name

NASA Ames Research Center

Department

Lab

NASA Ames Genome Research Facility

Street address

City

Moffett Field

State/province

CA

ZIP/Postal code

94043

Country

USA

Samples (6)

GSM38905, GSM38906, GSM38907, GSM38908, GSM38909, GSM38910

Series (1)

Chlamy genome wide transcription

Data table header descriptions
ID
X	X coordinate of the array feature
Y	Y coordinate of the array feature
SEQUENCE	DNA sequence of oligonucleotide
SCAFFOLD_NUMBER	Scaffold number
POSITION	Position of oligonucleotide in the scaffold sequence
STRAND	Strand of probe ('+' = Sense, '-' = Antisense)
FREQUENCY	Average frequency of probe in the genome
PROBE_TYPE	Type of probe (Exon = probe in coding region, Tiling = Probe in non-coding region, Random_probe = Random probe for background signal control, CONTROL = control probe for synthesis process and grid alignment)
EXON_CONFIDENCE	Confidence of the exon prediction (V = Verified, H = High confidence, L = Low confidence)
PROTEIN_NAME	Protein name

Data table
ID	X	Y	SEQUENCE	SCAFFOLD_NUMBER	POSITION	STRAND	FREQUENCY	PROBE_TYPE	EXON_CONFIDENCE	PROTEIN_NAME
1.1	1	1	CGTTCGGCGTGGACACGGCCAAGTGGATTTGCGTGT	19	265106	+	1.000000	Exon	V	158693
1.3	1	3	TATTCCAGCCTGTCACGAGTGCGTGTTGGCTTGCGC	729	6558	+	2.000000	Tiling	N/A	N/A
1.5	1	5	GTTGTACAACCAGTACCACGCGGTGCTGCTGGGCGA	20	526952	+	1.250000	Exon	V	159529
1.7	1	7	ACCTTGGGCGGCACCTGCTCGACTACTTTAGCGCTG	17	949247	-	1.000000	Exon	H	157916
1.9	1	9	ACGAGGTGCATGATGGGGTCTGGAAGCCTGCCCACT	146	180016	-	1.000000	Tiling	N/A	N/A
1.11	1	11	TTACACATGCACTGTTACCCCCCTTGCCTGCAGGTG	14	472258	-	1.100000	Tiling	N/A	N/A
1.13	1	13	ATCACAGTGCCTGGCTGTCTGTCAGCGGTGCCTGTG	3	1126138	-	1.000000	Exon	V	164669
1.15	1	15	AACGTTAACCCCCTACGCCTCCTCCTCTCCTCAGGT	111	197104	+	1.100000	Tiling	N/A	N/A
1.17	1	17	GTGCACGTGTTCCGTGTCGTTCGCTAGGCGCATTAG	1	1943489	-	2.000000	Tiling	N/A	N/A
1.19	1	19	CATGCCGCACGTGAACGTGGGTGACCTGCTGTTCGA	16	360650	-	1.000000	Exon	V	157346
1.21	1	21	AGACGCCACTCTTCACCATGCCGGTGGAGAAGGAGG	45	87460	-	1.000000	Exon	V	165616
1.23	1	23	AGCGCGTTGGCCTCGCCTTCCAAATCGGTGCTCACT	35	612838	+	1.000000	Exon	V	163783
1.25	1	25	TGACGACTTTGTCTGAGGATTCTTGCGCTCATTCAT	49	77445	+	1.000000	Tiling	N/A	N/A
1.27	1	27	TGCAGGGCCAAGGATGCCCATATGCAGGAGATGCAG	2	1694325	-	1.000000	Exon	V	162634
1.29	1	29	AAAGGAGGAGGACAAGGAGGAGGGCGTGGGTCAAGG	36	398200	-	3.100000	Tiling	N/A	N/A
1.31	1	31	ACACACATACGAACGTTGCGGTCGGCTCCCAAGGCC	172	79841	-	1.000000	Tiling	N/A	N/A
1.33	1	33	AAGCTCTCCGACTGCAATGGCCCGATGAGCCCTCGT	10	963512	-	1.300000	Exon	V	153257
1.35	1	35	ATGGCAGACACGACATATTAACTATTTCCGAAGACC	16	71592	-	1.000000	Tiling	N/A	N/A
1.37	1	37	ACGCAGCACGTGTATGTTGCACGCAACCCTCGCACG	35	110645	-	1.000000	Tiling	N/A	N/A
1.39	1	39	CACCTCCTCCTGCCGCCGCCGCCTCGCCATCCTTTA	111	226865	-	16.350000	Exon	V	153363

Total number of rows: 390886

Table truncated, full table size 33542 Kbytes.

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Supplementary data files not provided

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