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Platform GPL18536 Query DataSets for GPL18536
Status Public on Apr 08, 2014
Title Functional gene array for anaerobic Hanford 100H aquifer community
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism mixed sample
Manufacturer NimbleGen
Manufacture protocol High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
 
Description design name: 130110_Hanford_aquifer_UK_CGH
Custom 6x630k CGH design for Hanford aquifer community sequences. 313708 60mer probes were selected for the 44964 sequences provided by the customer. 7 probes were selected for 44618 sequences, 6 probes were selected for 95 sequences, 5 probes for 69 sequences, 4 probes for 58 sequences, 3 probes for 44 sequences, 2 probes for 36 sequences and 1 probe for 31 sequences. Probes were laid out in 2 replicates in containers BLOCK1 and BLOCK2. The remaining space on the array was filled with randomly-generated negative control probes of comparable length and composition.
native array description file: 130110_Hanford_aquifer_UK_CGH.ndf
native array description file: 130110_Hanford_aquifer_UK_CGH.pos
native array description file: 130110_Hanford_aquifer_UK_CGH_UX6.ncd
 
Submission date Apr 07, 2014
Last update date Apr 08, 2014
Contact name Ulas Karaoz
E-mail(s) ukaraoz@lbl.gov
Organization name LBNL
Street address 1 Cyclotron Rd.
City Berkeley
ZIP/Postal code 94720
Country USA
 
Samples (2) GSM1363713, GSM1363714
Series (1)
GSE56554 Expression analysis in anaerobic Hanford 100H aquifer flow-through columns receiving lactate and chromate

Data table header descriptions
ID SEQ_ID
function Putative function of the protein coded by the ORF to which the indicated probe is directed.
ORGANISM Putative taxonomic origin of the protein coded by the ORF to which the indicated probe is directed.
SPOT_ID

Data table
ID function ORGANISM SPOT_ID
T5_133_106417_376_1046:23_24_26_27:1-666 protein of unknown function UPF0005 Pseudomonas putida W619 protein of unknown function UPF0005
T5_76_60860_20265_20780_minus:21:1-510 major facilitator family transporter Pseudomonas syringae pv. tomato str. DC3000 major facilitator family transporter
N53B_452_11062_10634_11051_minus:15:1-414 conserved hypothetical protein Thermobaculum terrenum ATCC BAA-798 conserved hypothetical protein
HCN1_105_86848_82116_83:23_24_26_27:1-1050 Biotin synthase Pseudomonas savastanoi pv. savastanoi NCPPB 3335 Biotin synthase
HCN1_44_70586_30061_305:23_24_26_27:1-510 major facilitator family transporter Pseudomonas syringae pv. tomato str. DC3000 major facilitator family transporter
HCN1_1_51346_45204_4580:23_24_26_27:1-597 conserved hypothetical protein Pseudomonas aeruginosa 2192 conserved hypothetical protein
T5_364_25689_19646_20635_minus:21:1-981 OprF Pseudomonas chlororaphis subsp. chlororaphis OprF
T5_76_60860_34979_35518_minus:21:1-534 PA4251 synthetic construct PA4251
N53B_1857_6621_1391_2535_plus:14:1-1140 nitrite reductase, copper-containing Sinorhizobium medicae WSM419 nitrite reductase, copper-containing
T5_448_35905_6412_6729:23_24_26_27:1-312 hypothetical protein Pmen_3785 Pseudomonas mendocina ymp hypothetical protein Pmen_3785
HCN1_154_8884_2584_2907:23_24_26_27:1-318 co-chaperone Hsc20 Pseudomonas syringae pv. phaseolicola 1448A co-chaperone Hsc20
HCN1_241_26094_14741_15:23_24_26_27:1-435 nitric oxide reductase, NorB subunit apoprotein Magnetococcus sp. MC-1 nitric oxide reductase, NorB subunit apoprotein
N53B_115_29833_3916_445:23_24_26_27:1-534 PA4251 synthetic construct PA4251
T5_484_26146_14737_1517:23_24_26_27:1-435 nitric oxide reductase, NorB subunit apoprotein Magnetococcus sp. MC-1 nitric oxide reductase, NorB subunit apoprotein
HCN1_241_26094_17126_18:23_24_26_27:1-1668 nitrite reductase (NO-forming) Thiobacillus denitrificans ATCC 25259 nitrite reductase (NO-forming)
T5_484_26146_13313_1473:23_24_26_27:1-1416 nitric oxide reductase, NorB subunit apoprotein Magnetococcus sp. MC-1 nitric oxide reductase, NorB subunit apoprotein
HCN1_227_32087_17725_18:23_24_26_27:1-735 Osmolarity sensor protein envZ Pseudomonas mendocina ymp Osmolarity sensor protein envZ
N53B_2670_4947_1_1077_plus:15:1-1074 porin Ochrobactrum anthropi ATCC 49188 porin
T5_211_73894_18317_1942:23_24_26_27:1-1107 Alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase Pseudomonas putida F1 Alcohol dehydrogenase class III/S-(hydroxymethyl)glutathione dehydrogenase
HCN1_83_77333_22196_225:23_24_26_27:1-333 probable secretion pathway ATPase Pseudomonas stutzeri A1501 probable secretion pathway ATPase

Total number of rows: 44951

Table truncated, full table size 5993 Kbytes.




Download family Format
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MINiML formatted family file(s) MINiMLHelp

Supplementary file Size Download File type/resource
GPL18536_130110_Hanford_aquifer_UK_CGH.ndf.gz 48.3 Mb (ftp)(http) NDF
GPL18536_130110_Hanford_aquifer_UK_CGH.pos.gz 3.7 Mb (ftp)(http) POS
GPL18536_130110_Hanford_aquifer_UK_CGH_UX6.ncd.gz 296 b (ftp)(http) NCD

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