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Sample GSM480458 Query DataSets for GSM480458
Status Public on Jun 01, 2010
Title Sinorhizobium meliloti hfq deletion mutant, biological rep1
Sample type RNA
 
Source name hfq deletion mutant, cells harvested at OD600 of 0.87
Organism Sinorhizobium meliloti
Characteristics genotype/variation: 1021Dhfq
lab of origin: Max Teplitski
Treatment protocol Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.
Growth protocol For each biological replicate, a single bacterial colony was inoculated into 20 milliliters of TY broth, supplemented with streptomycin at 500 micrograms per microliter, and grown with shaking at 200 rpm at 30 degrees celsius in a 250 milliliter baffled flask.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.
Label biotin
Label protocol cDNA was fragmented and biotinylated as described by Barnett et al. 2004.
 
Hybridization protocol Four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G
Description Sinorhizobium meliloti hfq deletion mutant, biological rep1
Data processing The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.
 
Submission date Dec 07, 2009
Last update date Dec 07, 2009
Contact name Melanie J Barnett
Organization name Stanford University
Department Biology
Lab Sharon R. Long
Street address 371 Jane Stanford Way
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL9757
Series (1)
GSE19346 Expression data from wildtype Sinorhizobium meliloti Rm1021 and an hfq mutant

Data table header descriptions
ID_REF
VALUE GCOS v1.4 signal intensity
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
14523062i14523064f1_x_at 1651.8 P 0.005859
14523064i14523065f1_x_at 492.7 P 0.018555
14523064i14523065f2_x_at 24.8 A 0.466064
14523066i14523067f1_x_at 58 A 0.652557
14523066i14523067f2_x_at 1072.5 P 0.002371
14523067irna62f1_x_at 257.3 P 0.021484
14523067irna62f2_x_at 298.6 P 0.047363
14523070i14523071f1_x_at 344.3 A 0.126953
14523072i14523074f1_x_at 95.9 A 0.230957
14523074i14523075f1_x_at 625.9 P 0.000732
14523077i14523078f1_x_at 91.9 A 0.25
14523079i14523080f1_x_at 106.4 A 0.262207
14523081i14523082f1_x_at 43.9 A 0.567383
14523081i14523082f2_x_at 138.5 A 0.137695
14523085i14523087f1_x_at 9.9 A 0.738281
14523091i14523092f1_x_at 58.7 A 0.382813
14523095i14523096f1_x_at 176 A 0.251953
14523102i14523104f1_x_at 98.1 A 0.230469
14523105i14523106f1_x_at 654.4 P 0.042969
14523108i14523109f1_x_at 51.6 A 0.3125

Total number of rows: 12080

Table truncated, full table size 419 Kbytes.




Supplementary file Size Download File type/resource
GSM480458.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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