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| Status |
Public on Aug 14, 2024 |
| Title |
cciO replicate 1 |
| Sample type |
SRA |
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| Source name |
CB15
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| Organism |
Caulobacter vibrioides |
| Characteristics |
cell line: CB15
genotype: {delta}cciO
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| Treatment protocol |
Wildtype CB15, ΔcciO (CCNA_00027) and ΔcciT (CCNA_00028) (strains) were grown overnight in 2 mL of M2X medium containing the standard 10 µM Fe•EDTA chelate. These cultures were used to inoculate 10 mL of M2X to an OD660 of 0.001, which was then incubated overnight. After the OD660 exceeded 0.1, cells were collected by centrifugation, rinsed with iron-free M2X medium, and resuspended in 10 mL of M2X medium containing 10 µM FeCl3. The suspension was adjusted to an OD660 of 0.1 before incubation at 30˚C, shaken at 200 RPM for 2.5 hours.
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| Growth protocol |
CB15 cells were grown in M2X broth. Growth in M2X with 10 μM FeCl3.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested by centrifugation and stored at -80˚C until RNA extraction. RNA was extracted using TRIzol (Invitrogen) as previously described
RNA-sequencing libraries were prepared utilizing the Illumina TruSeq Stranded RNA Kit and sequenced on the Illumina NextSeq 500 platform at SeqCoast Genomics (Portsmouth, NH).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
SCD_421
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| Data processing |
CLC Genomic Workbench 20
Raw read files were imported with paired reads option with a minimum distance of 1 and a maximum distance of 1000. Failed reads where remove using NCBI/Sanger or Illumna Pipeline 1.8 and later setting
Reads were mapped to Caluobacter Crescentus genome CP001340 with the following parameters: Mismatch cost 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.8, Similarity fraction 0.8, Select Auto-detect paired distances, and Maximum number of hits for a read: 10
Read counts were extracted and normalized in CLC Genomic Workbench
Assembly: CP001340
Supplementary files format and content: comma-delimited files containing RAW, RPKM, TPM, and CPM counts for each sample.
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| Submission date |
Aug 07, 2024 |
| Last update date |
Aug 14, 2024 |
| 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 |
GPL24555 |
| Series (1) |
| GSE274268 |
A co-conserved gene pair supports Caulobacter iron homeostasis and resistance to chelation stress |
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| Relations |
| BioSample |
SAMN43071741 |
| SRA |
SRX25633768 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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