|
| Status |
Public on Jan 25, 2024 |
| Title |
JC2307 (DccrM Ptac-ccrM) ATGN-IPTG replicate C |
| Sample type |
SRA |
| |
|
| Source name |
JC2307
|
| Organism |
Agrobacterium tumefaciens |
| Characteristics |
cell line: JC2307
genotype: DccrM Ptac-ccrM
treatment: ATGN - IPTG
|
| Growth protocol |
Cells were cultivated exponentially for 7 hours in ATGN medium +/-IPTG 1mM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted from 1-2mL of bacterial cultures and immediately frozen in liquid nitrogen prior to conservation at -80°C. RNA were extracted using an RNeasy Mini-Kit from Qiagen and following the manufacturer’s protocol and including a DNase I (RNase-free DNases set from Qiagen) treatment. Samples were additionally treated with a TURBO DNA-free kit from Invitrogen following the manufacturer’s protocol.
RNA-seq libraries were prepared from 800 ng of total RNA with the TruSeq Stranded mRNA Prep reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on the Sciclone liquid handling robot (PerkinElmer). The polyA selection step was replaced by an rRNA depletion step with the QIAseq FastSelect - 5S/16S/23S bacterial rRNA removal kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
bcl2fastq2 Conversion Software (version 2.20, Illumina)
reads mapping on ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1)
reads were filtered for low complexity with reaper (v. 15-065)
reads genome mapping with STAR 42 (v. 23 2.5.3a)
number of read counts per gene locus was summarized with htseq-count 43 (v.0.9.1)
Assembly: Agrobacterium fabrum C58 ASM9202v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
|
| |
|
| Submission date |
Jan 12, 2024 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Karolina Bojkowska |
| E-mail(s) |
karolina.bojkowska@unil.ch
|
| Phone |
+41216923945
|
| Organization name |
University of Lausanne
|
| Lab |
Lausanne Genomic Technologies Facility
|
| Street address |
Unil, Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL34084 |
| Series (1) |
| GSE253175 |
RNA-seq gene expression profiling comparing WT and DccrM Ptac-ccrM Agrobacterium tumefaciens C58 cells cultivated in ATGN+/-IPTG. |
|
| Relations |
| BioSample |
SAMN39420836 |
| SRA |
SRX23202409 |
