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| Status |
Public on May 30, 2023 |
| Title |
∆essRS replicate 1 |
| Sample type |
SRA |
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| Source name |
cells
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| Organism |
Brucella ovis |
| Characteristics |
tissue: cells
genotype: BOV_1472 deletion mutant
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| Growth protocol |
Cells were started at OD600 = 0.05 in 12 ml Brucella broth and incubated on rotor at 37˚C with 5% CO2 for 7h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were incubated on rotor at 37˚C in 5% CO2 for 7h. 9 ml of each culture were spun down and the pellets were resuspended in 1 ml TRIzol. Samples were stored at -80˚C until RNA extraction. To extract the RNA, samples were thawed and incubated at 65˚C for 10 minutes. 200 µl of chloroform was added to each sample and mixed by vortexing for 15 seconds. Samples were then incubated at room temperature for 5 minutes. Samples were spun at 17,000 x g for 15 minutes at 4˚C and the aqueous layer was collected. Sample was mixed with 500 µl isopropanol and stored at -20˚C for 2h. After thawing, samples were spun down at 13, 300 x g for 30 minutes at 4˚C. Supernatants were discarded and 1 ml of ice cold 70% ethanol was added. Samples were spun down at 13,300 x g at 4˚C for 5 minutes. Supernatants were discarded and pellets were let completely dry. 100 µl RNAse-free H2O was added to each sample and incubated at 60˚C for 10 minutes. RNA samples were cleaned up using RNeasy Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Data processing |
CLC Genomic Workbench 21.0.4
Paired-end sequences were mapped to NC_009504 and NC_009505 using CLC Genomic Workbench (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
RPKM, TPM, CPM, and total counts of each replicate was calculated using the gene expression tool in CLC Genomic Workbench
Assembly: NC_009504 and NC_009505
Supplementary files format and content: excel file, contains RPKM, TPM, CPM, and total counts of each replicate
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| Submission date |
Apr 07, 2023 |
| Last update date |
May 30, 2023 |
| Contact name |
Sean Crosson |
| E-mail(s) |
[email protected]
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| Phone |
5178845345
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| Organization name |
Michigan State University
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| Department |
Dept. Microbiology and Molecular Genetics
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| Street address |
567 Wilson Rd
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| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL33317 |
| Series (2) |
| GSE229181 |
A unique mode of cross regulation in a cell envelope stress signaling system [RNA-seq] |
| GSE229183 |
A unique mode of cross regulation in a cell envelope stress signaling system |
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| Relations |
| SRA |
SRX19907954 |
| BioSample |
SAMN34116606 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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