|
| Status |
Public on Jun 08, 2016 |
| Title |
codY BHI 1 |
| Sample type |
SRA |
| |
|
| Source name |
codY BHI
|
| Organism |
Listeria monocytogenes 10403S |
| Characteristics |
genotype: codY (LMRG_00730) deletion mutant
medium: Rich (BHI)
|
| Growth protocol |
L. monocytogenes were grown to mid exponenital growth phase (OD 600nm = 0.3) in BHI or low BCAAs minimal medium (LBMM) and then harvested for RNA exctraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAsnap method followed by rRNA depletion using Epicentre RiboZero kit.
RNA-Seq libraries were prepared using the TruSeq RNA sample Prep kit™ (Illumina®)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNA depleted total RNA
|
| Data processing |
Quality control using the SeqMonk software
Trimming if needed using the FASTX tool kit
Alignment using Rockhopper software V1.3
Differential expression analysis using Rockhopper software V1.3
Genome_build: Listeria monocytogenes 10430S genome (the Broad Institute)
Supplementary_files_format_and_content: RPKM values with DE analysis
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lior Lobel |
| E-mail(s) |
liorlabe@post.tau.ac.il
|
| Organization name |
Tel Aviv University
|
| Department |
Molecular Microbiology
|
| Lab |
Anat Herskovits
|
| Street address |
Ramat Aviv
|
| City |
Tel Aviv |
| State/province |
Israel |
| ZIP/Postal code |
69978 |
| Country |
Israel |
| |
|
| Platform ID |
GPL20912 |
| Series (1) |
| GSE76159 |
Systems level analyses establish CodY as a multifaceted metabolic regulator integrating metabolism, motility and virulence in Listeria monocytogenes |
|
| Relations |
| BioSample |
SAMN04351080 |
| SRA |
SRX1491901 |
