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Sample GSM871903 Query DataSets for GSM871903
Status Public on Feb 17, 2012
Title AMB-1 ΔctrA
Sample type RNA
 
Source name Magnetospirillum magneticum str. AMB-1 ΔctrA
Organism Paramagnetospirillum magneticum AMB-1
Characteristics genotype/variation: ΔctrA
motility: non-motile
growth conditions: MG
Treatment protocol All strains grown identically, excepting the addition carbenicillin for strains carrying plasmids.
Growth protocol All strains were grown to mid-exponential phase (OD400 0.04 to 0.08) in 50 mL conical tubes in magnetospirillum growth media (MG) amended with 1/100 volume Wolfe's vitamin solution and 1/100 volume 3mM ferric 9mM malate. For ΔctrA deletion strains complemented with CtrA alleles, carbenicillin was added to 20ug/mL.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Trizol reagent as directed, DNase treated, and purified using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). RNA quality and concentration was determined by analysis with NanoDrop. cDNA was reverse transcribed using the Invitrogen Super Script RT III kit as directed and purified using a Qiagen PCR Clean Up kit.
Label cy3
Label protocol 0.5µg cDNA was fluorescently-labeled with Cy3 using the Nimblegen One Color DNA Labeling kit as directed.
 
Hybridization protocol Hybridization was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.
Scan protocol Scanning was performed by Fred Hutchinson Cancer Research Center, according to the standard operating protocol of NimbleGen Systems Inc., Madison, WI, USA.
Description CtrA 3
Nimb4PA01_dCtrA_3_415616_532.pair
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Feb 08, 2012
Last update date Feb 17, 2012
Contact name Arash Komeili
E-mail(s) komeili@berkeley.edu
Phone 510-642-2140
Organization name UC Berkeley
Department Plant and Microbial Biology
Lab Komeili
Street address 111 Koshland Hall #3102
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL15199
Series (1)
GSE35625 Expression analysis of Magnetospirillum magneticum AMB-1 WT, ΔMAI, ΔctrA, ΔdivK, and ΔctrA complemented with CtrA D51E, CtrA D51A, and an empty vector control

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity (RMA calls)

Data table
ID_REF VALUE
LD10_amb1008_amb1014_1070046_1070339 9.3682
LD11_amb1015_amb1018_1075142_1075708 12.1909
LD13_amb1026_amb1031_1091305_1090352 10.601
LD13_amb1026_amb1031_1092108_1092449 11.2415
LD1_amb0933_amb0941_1000521_1000664 9.1746
LD1_amb0933_amb0941_1000624_1001148 12.4775
LD1_amb0933_amb0941_999169_999474 9.155
LD2_amb0942_amb0949_1012526_1012876 11.1047
LD2_amb0942_amb0949_1012739_1013047 11.0597
LD6_amb0979_amb0993_1040560_1039265 11.0059
LD6_amb0979_amb0993_1047290_1049650 10.4956
LD7_no_ORFs_annotated_1050077_1060490 11.0842
LD7_no_ORFs_annotated_1051136_1051576 10.1756
LD7_no_ORFs_annotated_1053698_1052136 11.1036
LD7_no_ORFs_annotated_1054569_1053712 10.5733
LD7_no_ORFs_annotated_1054581_1055096 10.7905
LD8_amb0994_amb1001_1055440_1056360 11.8696
LD8_amb0994_amb1001_1056558_1056959 10.4888
LD8_amb0994_amb1001_1061118_1061810 11.945
LD8_amb0994_amb1001_1062536_1062712 9.9617

Total number of rows: 9040

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM871903.pair.gz 1.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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