|
| Status |
Public on Aug 02, 2024 |
| Title |
ΔvanAB pBVMCS6-AbnZ 15´Vanillate-R3 |
| Sample type |
SRA |
| |
|
| Source name |
CB15N
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
strain: CB15N
genotype: {delta}vanAB pBVMCS6-AbnZ
treatment: 500 uM Vanilalte
|
| Treatment protocol |
500 µM Vanillate, 15´
|
| Growth protocol |
Growth in PYE-Medium, 200 rpm shaking, 30 °C until OD 0.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction using the Hot Phenol methode, following DNase treatment/Pci extraction, rRNAdepletion and mRNA purification
RNA libraries for RNAseq were prepared using NEBNext® Small RNA Library Prep Set for Illumina® following manufacturer´s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
CC_KFS1421_Vanillate_R3
|
| Data processing |
Pipeline for RNAseq analysis CLC Genomics Workbench 22.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomics Workbench 22.0.2 (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to NC_011916.1 using CLC Genomics Workbench 22.0.2 (parameters-mismatch cost:2 insertion cost:3 deletion cost:3 lenght fraction: 0.8 similarity fraction: 0.8 strand specific:rev)
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NCBI Reference Sequence: NC_011916.1
Supplementary files format and content: xlsx file including TPM from each sample
|
| |
|
| Submission date |
Jun 24, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Manuel Velasco Gomariz |
| E-mail(s) |
[email protected]
|
| Organization name |
Friedrich Schiller University Jena
|
| Street address |
Winzerlaer Str. 2
|
| City |
Jena |
| ZIP/Postal code |
07743 |
| Country |
Germany |
| |
|
| Platform ID |
GPL34591 |
| Series (1) |
| GSE270559 |
An sRNA overexpression library reveals AbnZ as a negative regulator of an essential translocation module in Caulobacter crescentus |
|
| Relations |
| BioSample |
SAMN42048028 |
| SRA |
SRX25059242 |
