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Platform GPL16974 Query DataSets for GPL16974
Status Public on Nov 28, 2013
Title NimbleGen custom Bacillus subtilis MAD-BS-2-Nimble-E-135
Technology type in situ oligonucleotide
Distribution custom-commercial
Organism Bacillus subtilis
Manufacturer NimbleGen
Manufacture protocol Details on the manufacture protocol can be found on http://www.nimblegen.com/technology/index.html
 
Description Design settings: Design based on NCBI Bacillus subtilis 168 uid57675 fasta sequence (26 jan 2011, Refseq:NC_000964.3, gi|255767013). Maximum of 135.000 probes. Design on both strands Probe length 60 bases Blast bitscore threshold of 80. Design results: 131.580 probes designed. Resulting tile-step of 32 bases. Overlap of 28 bases between probes (=gap-size -28) on opposite strands. Gap size of 4 bases between probes on the same strand. 303 Spike-in probes for 8 spike-in mRNA’s. 6.400 control probes (5000 “Alien” negative controls + 1400 Concentration Controls)
 
Submission date Apr 05, 2013
Last update date Jul 19, 2020
Contact name Martijs Jonker
E-mail(s) m.j.jonker@uva.nl
Organization name University of Amsterdam
Department Microarray Department
Street address Science Park 904
City Amsterdam
ZIP/Postal code 1090 GE
Country Netherlands
 
Samples (29) GSM1116043, GSM1116044, GSM1116045, GSM1116046, GSM1116047, GSM1116048 
Series (2)
GSE45824 The conserved DNA-binding protein WhiA is involved in cell division in Bacillus subtilis
GSE146277 Intergrative analysis of proteome and transcriptome dynamics during Bacillus subtilis spore revival

Data table header descriptions
ID IDs of the genes
ORF Locustag
SPOT_ID spot id
FRAME.ID Frame ID
NAME Probe Name
Names Probe Names
Synonyms Probe Synonyms
Product Products
Left.End.Position Left End Position
Right.End.Position Right End Position
Transcription.Direction Direction of the transcription

Data table
ID ORF SPOT_ID FRAME.ID NAME Names Synonyms Product Left.End.Position Right.End.Position Transcription.Direction
BSU00010 BSU00010 BSU00010 dnaA dnaA, dnaH, dnaJ, dnaK dnaH, dnaJ, dnaK chromosomal replication initiator protein DnaA 410 1750 +
BSU00020 BSU00020 BSU00020 dnaN dnaN, dnaG, dnaK dnaG, dnaK DNA polymerase III (beta subunit) 1939 3075 +
BSU00030 BSU00030 BSU00030 yaaA yaaA putative RNA binding protein 3206 3421 +
BSU00040 BSU00040 BSU00040 recF recF DNA repair and genetic recombination factor 3437 4549 +
BSU00050 BSU00050 BSU00050 remB remB, yaaB yaaB regulator of the extracellular matrix 4567 4812 +
BSU00060 BSU00060 BSU00060 gyrB gyrB, novA novA DNA gyrase (subunit B) 4867 6783 +
BSU00070 BSU00070 BSU00070 gyrA gyrA, nalA nalA DNA gyrase (subunit A) 6994 9459 +
BSU00080 BSU00080 BSU00080 yaaC yaaC conserved hypothetical protein 14847 15794 -
BSU00090 BSU00090 BSU00090 guaB guaB, guaA guaA inosine-monophosphate dehydrogenase 15915 17381 +
BSU00100 BSU00100 BSU00100 dacA dacA D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) 17534 18865 +
BSU00110 BSU00110 BSU00110 pdxS pdxS, yaaD yaaD glutamine amidotransferase for pyridoxal phosphate synthesis 19062 19946 +
BSU00120 BSU00120 BSU00120 pdxT pdxT, yaaE yaaE glutamine amidotransferase for pyridoxal phosphate synthesis 19968 20558 +
BSU00130 BSU00130 BSU00130 serS serS seryl-tRNA synthetase 20880 22157 +
BSU00140 BSU00140 BSU00140 dck dck, yaaF yaaF deoxyadenosine/deoxycytidine kinase 22496 23149 -
BSU00150 BSU00150 BSU00150 dgk dgk, yaaG yaaG deoxyguanosine kinase 23146 23769 -
BSU00160 BSU00160 BSU00160 yaaH yaaH spore peptidoglycan hydrolase 23868 25151 -
BSU00170 BSU00170 BSU00170 yaaI yaaI putative isochorismatase 25221 25766 -
BSU00180 BSU00180 BSU00180 tadA tadA, yaaJ yaaJ tRNA specific adenosine deaminase 25852 26337 +
BSU00190 BSU00190 BSU00190 dnaX dnaX, dnaH, dna-8132 dnaH, dna-8132 DNA polymerase III (gamma and tau subunits) 26814 28505 +
BSU00200 BSU00200 BSU00200 yaaK yaaK DNA binding protein 28529 28852 +

Total number of rows: 4327

Table truncated, full table size 416 Kbytes.




Download family Format
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Supplementary file Size Download File type/resource
GPL16974_120105_Bacillus_RW_expr.ndf.gz 5.7 Mb (ftp)(http) NDF
GPL16974_Probe_file_MAD-BS-2-Nimble-E-135.txt.gz 3.1 Mb (ftp)(http) TXT
GPL16974_probe_annot_BS168.txt.gz 4.5 Mb (ftp)(http) TXT

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