|
| Status |
Public on Dec 01, 2020 |
| Title |
WT library grown in LB |
| Sample type |
SRA |
| |
|
| Source name |
Enterohemorrhagic E. coli (EHEC) colonies
|
| Organism |
Escherichia coli O157:H7 str. EDL933 |
| Characteristics |
genotype: WT
treatment: grown on LB plates
|
| Treatment protocol |
for selection, libraries were grown for 1 hour in liquid LB culture at 37C and then plated on either LB Kan 50 ug/mL or LB plates containing 1% DOC and Kan 50 ug/mL
|
| Growth protocol |
libraries were created on LB Kanamycin 50ug/mL plates at 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was isolated using Wizard Genomic DNA extraction kit
transposon-containing fragments were amplified with custom primers using PCR
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
processed file: fitness_in_doc.txt
|
| Data processing |
Library strategy: Tn-Seq, TIS
Reads were trimmed of transposon and adapter sequences in CLC Genomics Workbench
Reads were mapped to EHEC genome (chromosome NZ_CP008957.1, plasmid NZ_CP008958.1) using Bowtie, allowing for no mismatches
Data was processed using the ARTIST pipeline. Code available in Pritchard 2014 Plos Genetics 10(11):e1004782
Genome_build: chromosome NZ_CP008957.1, plasmid NZ_CP008958.1
Supplementary_files_format_and_content: matrix of ARTIST pipeline output
|
| |
|
| Submission date |
Nov 30, 2020 |
| Last update date |
Dec 01, 2020 |
| Contact name |
Matthew K Waldor |
| E-mail(s) |
mwaldor@research.bwh.harvard.edu
|
| Phone |
617-525-4660
|
| Organization name |
Harvard Medical School
|
| Department |
Microbiology
|
| Lab |
Waldor Lab
|
| Street address |
181 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL23073 |
| Series (1) |
| GSE162346 |
Genetic analysis of the role of the conserved inner membrane protein CvpA in EHEC resistance to deoxycholate |
|
| Relations |
| BioSample |
SAMN16960785 |
| SRA |
SRX9606477 |
