|
| Status |
Public on Jan 05, 2019 |
| Title |
TI: △tnaA EHEC with 500µM indole |
| Sample type |
SRA |
| |
|
| Source name |
EHEC
|
| Organism |
Escherichia coli O157:H7 |
| Characteristics |
strain: 86 24
genotype: tnaA deletion muant
treatment: indole
|
| Treatment protocol |
500µM of indole or only methanol in a dilution ratio of 1:1000 was added to the low gluocse DMEM before starting the experiment
|
| Growth protocol |
WT and △tnaA EHEC strains were grown in low gluocse DMEM until late log phase with either methanol or 500µM indole in three biological replicates. Samples were checked for similar O.D and then samples were harvested by centrfugation. The RNA was extracted from the pellet fraction using Ribopure RNA extraction kit (Ambion).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Ribopure RNA extraction kit (Ambion)
12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Our 12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
Sequencing run: Our 12 RNA libraries were run on illumine HiSeq 2500 sequencer with SE-50.
Raw data was processed using DNAStar Lasergene software as per the instructions provided on the DNAStar website
Genome_build: sakai genome downloaded from ncbi was used as a reference genome (NC_002695.1)
Supplementary_files_format_and_content: tab delimited text file includes the RKPM values for all samples under the conditions tested above.
Supplementary_files_format_and_content: .astar files can be accessed using DNAStar Lasergene software
|
| |
|
| Submission date |
Sep 04, 2018 |
| Last update date |
Jan 05, 2019 |
| Contact name |
Aman Kumar |
| E-mail(s) |
aman.kumar@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Microbiology
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390-9048 |
| Country |
USA |
| |
|
| Platform ID |
GPL25528 |
| Series (1) |
| GSE119440 |
Indole signaling at the host-microbiota-pathogen interface |
|
| Relations |
| BioSample |
SAMN09951429 |
| SRA |
SRX4637978 |
