GEO help: Mouse over screen elements for information.
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
GSM1116049 ,
GSM4376606 ,
GSM4376607 ,
GSM4376608 ,
GSM4376609 ,
GSM4376610 ,
GSM4376611 ,
GSM4376612 ,
GSM4376613 ,
GSM4376614 ,
GSM4376615 ,
GSM4376616 ,
GSM4376617 ,
GSM4376618 ,
GSM4376619 ,
GSM4376620 ,
GSM4376621 ,
GSM4376622 ,
GSM4376623 ,
GSM4376624 ,
GSM4376625 ,
GSM4376626 ,
GSM4376627 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
+
4327 416 Kbytes .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
Less...
More...