|
| Status |
Public on Apr 11, 2022 |
| Title |
RNASeq_CtrA_NA1000 DchvI_2 |
| Sample type |
SRA |
| |
|
| Source name |
DchvI
|
| Organism |
Caulobacter vibrioides |
| Characteristics |
strain: DchvI
treatment: Mid-exponential phase in synthetic complex medium (PYE) supplemented with 6% Sucrose
|
| Treatment protocol |
Then, 6% Sucrose were added and cells were incubated at 30°C for 4 hours.
|
| Growth protocol |
C. crescentus strains grown overnight at 30°C in complex media (PYE) to saturation before being diluted in fresh PYE media and grown at 30°C to mid-exponential phase (OD660~0.3).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted with RNeasy® Protect Bacteria Kit from Qiagen and following manufacturer’s instructions.
ChIP-Seq libraries were prepared at the BIO.be company (Belgium) using the RNASeq TTRNA library according to the manufacturer's instructions, after rRNA depletion and cDNA synthesis.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
transcriptomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Between 2 x 10^7 and 3 x 10^7 paired-end sequence reads (2 x 100) were first mapped on the genome of C. crescentus NA1000 (NC_011916.1) using Galaxy
The number of reads overlapping each genomic position was computed using Galaxy
A DESeq2 analysis was then peformed between the WT and DchvI samples using Galaxy
Assembly: NC_011916.1
Supplementary files format and content: The xls files report ChvI RNA-Seq regulon with Fold Change (FC) between WT and DchvI strains. The different columns are organized as follows: column 1: Gene_ID (CCNA gene identification number); column 2: Name (Predicted function of the corresponding gene); column 3: Base_mean (mean of normalized counts); column 4: log2(FC_WT/DchvI) (base 2 log of fold change between WT and DchvI); column 5: P-value; column 6: P-adj (adjusted P-value); column 7: FC_WT/DchvI (fold change between WT and DchvI); column 8: FC_DchvI/WT (fold change between DchvI and WT); column 9: log2(FC_DchvI/WT) (base 2 log of fold change between DchvI and WT); column 10: -(log_FDR) (-base10 log of false discovery rate)
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| |
|
| Submission date |
Apr 08, 2022 |
| Last update date |
Apr 11, 2022 |
| Contact name |
Regis Hallez |
| E-mail(s) |
[email protected]
|
| Organization name |
UNamur
|
| Street address |
61 Rue de Bruxelles
|
| City |
Namur |
| ZIP/Postal code |
5000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL32153 |
| Series (2) |
| GSE200464 |
The two-component system ChvGI responds to osmotic upshift and peptidoglycan damage in Caulobacter crescentus [RNA-seq] |
| GSE200466 |
The two-component system ChvGI responds to osmotic upshift and peptidoglycan damage in Caulobacter crescentus. |
|
| Relations |
| BioSample |
SAMN27413002 |
| SRA |
SRX14786001 |
