|
| Status |
Public on Mar 09, 2024 |
| Title |
plus_cmdTAC_15min_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
str. K12 substr. MG1655
|
| Organisms |
Escherichia coli; Escherichia phage T4 |
| Characteristics |
tissue: str. K12 substr. MG1655
genotype: pKVS45-cmdTAC
treatment: T4 infection
|
| Treatment protocol |
Cultures at an OD600 between 0.2 and 0.3 were infected with bacteriophage T4 at a multiplicity of infection (MOI) of 10 and continued to grow at 37C with shaking at 200rpm until sample collection. Samples were collected by mixing 1 mL of cells with 1 mL of of boiling lysis buffer (2% SDS, 4 mM EDTA) before flash freezing in liquid nitrogen.
|
| Growth protocol |
Overnight cultures of +cmdTAC and -cmdTAC cells were grown at 37C in LB + chloramphenicol. The day of the experiment cultures were back-diluted to an OD600 = 0.05 and allowed to grow for an additional 1.5 hours in LB + chloramphenicol at 37C until reaching an OD600 between 0.2 and 0.3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with two rounds of acidic phenol heated to 67C followed by one extraction with acidic phenol chloroform at room temperature. RNA was precipitated using isopropanol precipitation at -80C and DNA was removed with DNAse treatment using Turbo DNAse. rRNA was depleted using biotinylated capture probes specific to the E. coli 5S, 16S, and 23S rRNA
cDNA library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer's protocol fro use with rRNA depleted RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Remaining adapter sequences were trimmed from reads using cudadapt. Paired-end reads were mapped to the MG1655 (NC_00913.2) and T4 (NC_000866) genomes using bowtie2 and default settings. Mapped reads were converted into python operable numpy arrays using the python package genomearray3. TPM calculations were performed using the custom made jupyter notebooks available at https://github.com/chrisdoering8197/CmdTAC.
Assembly: NC_00913.2, NC_000866
Supplementary files format and content: TPM values for each gene in addition to the gene name are listed for both the MG1655 genome (rnaseq_host_tpm.csv) and T4 genome (rnaseq_t4_tpm.csv)
|
| |
|
| Submission date |
Jan 17, 2024 |
| Last update date |
Mar 09, 2024 |
| Contact name |
Christopher Ross Doering |
| E-mail(s) |
cdoering@mit.edu
|
| Organization name |
MIT
|
| Department |
Biology
|
| Lab |
Michael Laub
|
| Street address |
31 Ames St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL34102 |
| Series (2) |
| GSE253513 |
Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation (RNA-Seq) |
| GSE253514 |
Anti-viral defense by an ADP-ribosyltransferase that targets mRNA to block translation |
|
| Relations |
| BioSample |
SAMN39476104 |
| SRA |
SRX23265807 |
