|
| Status |
Public on May 10, 2023 |
| Title |
160108_3200: Sinorhizobium meliloti JOE3200, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Rm1021 strain carrying the empty vector, pCM130 (control strain)
|
| Organism |
Sinorhizobium meliloti |
| Characteristics |
strain: JOE3200
genotype/variation: carrying the empty vector, pCM130 (control strain)
|
| 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 |
Starter cultures were grown overnight in PYE medium with 0.5 ug ml-1 oxytetracycline; diluted to ~0.25 to ~0.30 OD-600 in 25 ml of the same medium with 10 mM taurine, in 125-ml flasks; and allowed to grow for 4.5 hours, shaken (250 rpm) at 30°C, to mid-exponential phase (~0.5 to ~0.7 OD-600), with replicates from a single experiment grown to within ~0.1 OD-600 units of each other, prior to harvest.
|
| 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
|
| Data processing |
The data were analyzed using Partek Genomics Suite 6.6 software, with the following settings: RMA for background correction; quantile normalization; log base 2 transformation; median polish summarization
|
| |
|
| Submission date |
Aug 06, 2020 |
| Last update date |
May 12, 2023 |
| 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) |
| GSE155833 |
Identifying the regulon of the Sinorhizobium meliloti JspA protease |
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