NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Platform GPL5776 Query DataSets for GPL5776
Status Public on Aug 26, 2008
Title Earthworm 4K cDNA array version 1.1
Technology type spotted DNA/cDNA
Distribution non-commercial
Organism Eisenia fetida
Manufacturer USACE-ERDC-EL Environmental Genomics and Genetics team
Manufacture protocol 1. A total of 4032 purified cDNA clones were loaded on 384-well plates and completely dried down in a Vacufuge Concentrator 5301 (Eppendorf, Westbury, NY).
2. The dried cDNA was re-suspended in 15ul of 1¡Á printing buffer (ArrayIt, Sunnyvale, CA).
3. Each clone was spotted twice (i.e., in two super grids) on Ultra GAPS amino silane coated glass slides (Corning, Acton, MA) using 16 pins on a VersArray ChipWriter (Bio-Rad, Hercules, CA).
4. Five alien cDNAs, i.e., PCR product 1 to 5 selected from SpotReport Alien cDNA Array Validation System (Stratagene, La Jolla, CA) prepared at 15, 30, 60, 125 and 250 ng/ul were also spotted twice along with printing buffer and water as control spots.
5. The total number of spots on each array was 8704 including 60 alien cDNA spots, 84 water spots, 256 blank spots and 240 printing buffer spots.
6. After printing, arrays were incubated in a dessicator 2-3 days and were then snap-dried on a hot plate after being rehydrated over a boiling water bath.
7. The arrays were further immobilized using a UV Cross-linker (Stratagene) by applying 300 mJ per 10 arrays.
8. Printing time: May 12, 2006
Support Corning Ultra GAPS coated glass slide
Coating gamma amino propyl silane (GAPS)
 
 
Contributor(s) Gong P, Guan X, Pirooznia M, Indest KJ, Perkins EJ
Submission date Aug 27, 2007
Last update date Aug 26, 2008
Contact name Ping Gong
E-mail(s) ping.gong@us.army.mil
Phone (601) 634-3521
Organization name US Army ERDC
Department Environmental Laboratory
Lab Environmental Genomics and Genetics
Street address 3909 Halls Ferry Road
City Vicksburg
State/province MS
ZIP/Postal code 39180
Country USA
 
Samples (40) GSM225315, GSM225321, GSM225340, GSM225341, GSM225342, GSM225343 
Series (1)
GSE8909 Profiling differentially expressed earthworm genes in response to TNT, RDX, or TNT+RDX exposure.

Data table header descriptions
ID Spot number
dbEST_ID GenBank EST database ID number
CLONE ID
GB_ACC GenBank accession number of spotted cDNA
Contig_ID Assembled contig number
Hit_GB_Acc GenBank matching protein accession number
E_value Expectation value for matching protein
Gen_Desc Putative gene function description
Super_Grid Duplicated super grid number
Array_Grid Grid number on array
Array_Row Row number on array
Array_Col Column number on array
Spot_Loc Spot position (Grid-Row:Column)
SPOT_ID controls

Data table
ID dbEST_ID CLONE ID GB_ACC Contig_ID Hit_GB_Acc E_value Gen_Desc Super_Grid Array_Grid Array_Row Array_Col Spot_Loc SPOT_ID
1 EW1_R1P07_H05 1 1 1 1 1-1:1 ambiguous clone_EW1_R1P07_H05
2 44048070 EW1_R1P05_G01 EH671164 AAD30302.1 2.1 urokinase plasminogen activator receptor 1 1 1 2 1-1:2
3 44047882 EW1_R1P02_G09 EH670976 BAD91025.1 3E-61 valosin containing protein-2 1 1 1 3 1-1:3
4 44047011 EW1_F1P09_H05 EH670105 XP_694466.1 0.0003 PREDICTED: similar to RIKEN cDNA 4930429A22 1 1 1 4 1-1:4
5 44904747 EW1_F2P15_G01 EL515452 P81695 6E-22 MT_EISFO Cadmium-metallothionein (MT) 1 1 1 5 1-1:5
6 44047236 EW1_F2P12_G09 EH670330 Contig209 ******No hits 1 1 1 6 1-1:6
7 44046848 EW1_F1P07_H05 EH669942 Contig132 CAA58705.1 1E-34 intermediate filament protein 1 1 1 7 1-1:7
8 44046671 EW1_F1P05_G01 EH669765 Contig166 NP_001033116.1 0.000000002 glutamyl aminopeptidase (aminopeptidase A) 1 1 1 8 1-1:8
9 44046426 EW1_F1P02_G09 EH669520 NP_001006352.1 0.00000002 ADP-ribosylation factor 1 1 1 1 9 1-1:9
10 44049270 EW2_R1P11_H05 EH672364 AAA67037.1 4E-25 protein kinase 1 1 1 10 1-1:10
11 44049100 EW2_R1P09_G01 EH672194 AAH90516.1 4E-20 LOC553323 protein 1 1 1 11 1-1:11
12 44048891 EW2_R1P06_G09 EH671985 Contig424 CAE18118.1 2E-15 SCBP3 protein 1 1 1 12 1-1:12
13 44048651 EW2_R1P03_H05 EH671745 XP_953940.1 1.7 hypothetical protein TA05930 1 1 1 13 1-1:13
14 44048507 EW2_R1P01_G01 EH671601 XP_653341.1 3.6 receptor protein kinase 1 1 1 14 1-1:14
15 EW2_F1P01_G09 1 1 1 15 1-1:15 ambiguous clone_EW2_F1P01_G09
16 44047587 EW1_F1P18_A08 EH670681 Contig447 ******No hits 1 1 1 16 1-1:16
17 44047692 EW1_F1P20_B12 EH670786 AAH47987.1 4.8 Dj462o23.2-prov protein 1 1 1 17 1-1:17
18 44048178 EW1_R1P07_H09 EH671272 AAH59622.1 6E-40 Phosphopantothenoylcysteine decarboxylase 1 1 2 1 1-2:1
19 44048074 EW1_R1P05_G05 EH671168 XP_396744.2 1E-27 PREDICTED: similar to oocyte membrane protein 1 1 2 2 1-2:2
20 EW1_R1P02_H01 1 1 2 3 1-2:3 ambiguous clone_EW1_R1P02_H01

Total number of rows: 8704

Table truncated, full table size 778 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