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Platform GPL5883 Query DataSets for GPL5883
Status Public on Sep 21, 2007
Title WUSTL Caenorhabditis elegans Whole Genome 23k Oligo Array
Technology type spotted oligonucleotide
Distribution non-commercial
Organism Caenorhabditis elegans
Manufacturer washington university microarray core facility
Manufacture protocol General Information
Arrays printed on Corning Epoxy slides
Slides have been post-processed and are ready to hyb.
Common spot diameter – 90-110μ
Spot to spot distance – 200μ
• 22614 features
• 22490 oligo features
• 124 control features
• 12 Rows
• 4 Colums
• 48 Subarrays
Feature Concentration Information
A. thaliana Features printed at 50 uM
Controls (Positive and Negative) printed at 40 uM
Poly(dA)40–60 oligonucleotide printed at 0.01 μg/μL
Salmon sperm DNA printed at 0.1 μg/μL
Human COT-1 DNA® printed at 0.1 μg/μL
Control Feature Information
Control Oligonucleotides
Number Arabidopsis thaliana Gene Identification
Positive Controls (70-mer)
10 Oligonucleotide 1 (Cab) A. thaliana photosystem I chlorophyll a/b-binding
protein
(GenBank® database accession # X56062)
10 Oligonucleotide 2 (RCA) A. thaliana RUBISCO activase
(GenBank database accession #X14212)
10 Oligonucleotide 3 (rbcL) A. thaliana ribulose-1,5-bisphosphate
carboxylase/oxygenase large subunit
(GenBank database accession#U91966)
10 Oligonucleotide 4 (LTP4) A. thaliana lipid transfer protein 4
(GenBank database accession #AF159801)
10 Oligonucleotide 5 (LTP6) A. thaliana lipid transfer protein 6
(GenBank database accession #AF159803)
10 Oligonucleotide 6 (XCP2) A. thaliana papain-type cysteine endopeptidase
(GenBank database accession #AF191028)
10 Oligonucleotide 7 (RCP1) A. thaliana root cap 1
(GenBank database accession #AF168390)
10 Oligonucleotide 8 (NAC1) A. thaliana NAC1
(GenBank database accession #AF198054)
10 Oligonucleotide 9 (TIM) A. thaliana triosphosphate isomerase
(GenBank database accession #AF247559)
10 Oligonucleotide 10 (PRKase) A. thaliana PRKase gene for ribulose-5-phosphate
kinase
(GenBank database accession #X58149)
Negative Controls
10 E. coli – B1444 oligonucleotide
8 E. coli – rRNA oligonucleotide
2 Poly(dA)40–60 oligonucleotide
2 Salmon sperm DNA
1 Human COT-1 DNA®
1 3X SSC/0.75 M Betaine
124 – Total Control Features
 
 
Submission date Sep 17, 2007
Last update date Sep 21, 2007
Contact name liang zhang
E-mail(s) liangz@colorado.edu
Organization name university of colorado at boulder
Street address University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347
City Boulder
State/province CO
ZIP/Postal code 80309-0347
Country USA
 
Samples (163) GSM230859, GSM230860, GSM230861, GSM230862, GSM230863, GSM230864 
Series (8)
GSE9073 AIN-1 and AIN-2::GFP IP of C.elegans miRNA targets
GSE15923 C. elegans genomic response to Konza Prairie Soil bacterial environment
GSE16036 AhR mutant vs N2 wild-type C.elegans, in L1 larval stage

Data table header descriptions
ID
Probe Name The name of the spotted probe, refer to the supplemental files for sequence
Gene Name The corresponding annotated gene name in wormbase
ORF Locus tag
SEQUENCE oligo sequence
SPOT_ID controls

Data table
ID Probe Name Gene Name ORF SEQUENCE SPOT_ID
1 Spot Report 1 - Cab Spot Report 1 - Cab --CONTROL_Spot Report 1 - Cab
2 cea2.c.00914 C25A1.8 C25A1.8 tcgtttattatttgtcaccgggttccatcccccttacgtttgacaatcattgcactcact
3 cea2.c.02677 F21F3.6 F21F3.6 ctccatcccacacacacacacttgtccaaacccaatgtatatttctcggaatatccccga
4 cea2.c.02801 F25H2.9 F25H2.9 ggcgtccaatcggagaattcacaagagtgtcgaacgaagagctcgatcaagttatcacat
5 cea2.c.04344 F56H1.4 F56H1.4 tttcgtattctattcccacccctctcctgtttttattgattcatcctcgaagtgcgtgga
6 cea2.c.04508 H06O01.1 H06O01.1 tttggtgccttcattatggcgtttcgtacgccttttttgccaataaaccttctggtctct
7 cea2.c.06048 T20F10.2 T20F10.2 tcgccgagccagatgcagttgatggagatgagcaagacgacaaggagacataatttaaat
8 cea2.c.06316 T23H2.5 T23H2.5 ccacagaggcagagtagcagtggaggatgctgctagattcatgtttttccctcttacttc
9 cea2.c.07850 Y65B4BR.6 Y65B4BR.6 gttcccgccgttgccattcccctgacaaaaaatatggtcggcatttgtctgtacaaattg
10 cea2.c.08046 Y71F9B.8 Y71F9B.8 cctctttcccgtcaaactggtacttgccattccactgaaatgttccgattgttcaaacga
11 cea2.c.10006 C16A11.1 C16A11.1 cacgagaagcctctgtacacgcatataaccaatgcgacagacactcggaatattgatcgg
12 cea2.c.10341 C30B5.6 C30B5.6 tcattccctctctctcttgtttctctctgtctctcttcccttcccattgattcctttctt
13 cea2.c.11934 F33A8.2 F33A8.2 tgtttcccccttccaccaattccccccacgtcctaatgaaatgaaagcgagaagataaat
14 cea2.c.12152 F37H8.5 F37H8.5 gagacaaggccattccatactgtgaggctgctctcaaattgaagtacaagaaggccagta
15 cea2.c.13713 R07G3.1 R07G3.1 actgttttctcatccactacgttttgtgtctccctcctcctttctccagaacaactctgt
16 cea2.c.13904 T01E8.4 T01E8.4 cccatcatcgagaactctggcaattggcaatggtgatagctcaattctgttctgtcttcc
17 cea2.c.15361 Y48E1B.10 Y48E1B.10 tcccggagattcgcaagcatcttgaatcgagcccggataagggattctaatcattttctg
18 cea2.c.15549 Y54G9A.7 Y54G9A.7 caaccccagaagaagccgagcagatcaaggcgttgaaggagaaatacgcgaaattatatc
19 cea2.c.17394 C16A3.4 C16A3.4 ggcagtcaagtcgaacaagttgttcaagacaaacggattcgtcggagacaatcattgacc
20 cea2.c.17578 C28H8.12 C28H8.12 agcgattatcgagtatgagtcccaaggaaagcaagaaatcgggtcagtggttgaaaagct

Total number of rows: 23232

Table truncated, full table size 2178 Kbytes.






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