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Sample GSM871910 Query DataSets for GSM871910
Status Public on Feb 17, 2012
Title AMB-1 ΔctrA + ctrA D51A ampR rep3
Sample type RNA
 
Source name Magnetospirillum magneticum str. AMB-1 ΔctrA complemented with ctrA D51A (ampR)
Organism Paramagnetospirillum magneticum AMB-1
Characteristics genotype/variation: ΔctrA complemented with ctrA D51A
motility: non-motile
growth conditions: MG + 20ug/ml carbenicillin
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 D51A tb 6
Nimb4PA01_dCtrA+Atb_6_330368_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 9.2856
LD11_amb1015_amb1018_1075142_1075708 11.7199
LD13_amb1026_amb1031_1091305_1090352 10.7378
LD13_amb1026_amb1031_1092108_1092449 11.1333
LD1_amb0933_amb0941_1000521_1000664 9.0528
LD1_amb0933_amb0941_1000624_1001148 10.9184
LD1_amb0933_amb0941_999169_999474 10.0788
LD2_amb0942_amb0949_1012526_1012876 10.6137
LD2_amb0942_amb0949_1012739_1013047 10.1601
LD6_amb0979_amb0993_1040560_1039265 10.6007
LD6_amb0979_amb0993_1047290_1049650 11.3808
LD7_no_ORFs_annotated_1050077_1060490 11.8759
LD7_no_ORFs_annotated_1051136_1051576 9.7367
LD7_no_ORFs_annotated_1053698_1052136 10.5406
LD7_no_ORFs_annotated_1054569_1053712 10.6298
LD7_no_ORFs_annotated_1054581_1055096 11.42
LD8_amb0994_amb1001_1055440_1056360 11.6546
LD8_amb0994_amb1001_1056558_1056959 10.6066
LD8_amb0994_amb1001_1061118_1061810 11.3273
LD8_amb0994_amb1001_1062536_1062712 9.301

Total number of rows: 9040

Table truncated, full table size 251 Kbytes.




Supplementary file Size Download File type/resource
GSM871910.pair.gz 1.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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