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| Status |
Public on May 10, 2017 |
| Title |
401140_DMEM_0.5_BR1 |
| Sample type |
SRA |
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| Source name |
Escherichia coli cells
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| Organism |
Escherichia coli 401140 |
| Characteristics |
strain: 401140
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| Growth protocol |
The EPEC strains were grown overnight in Luria-Bertani (LB) media and were inoculated 1:100 into 250 ml of fresh LB or DMEM and were incubated with shaking (225 rpm) at 37˚C to a final optical density (OD600) of approximately 0.5.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells grown in LB or DMEM using the Ribopure Bacteria kit (Ambion) and contaminating DNA was removed using the Ribopure Dnase I and also the Turbo DNA-free kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina reads were mapped to the EPEC genomes using Bowtie
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
Genome_build: E2348/69, B171, C581-05, E110019, 401140, 402290, 401588, 302053, 100329, 103385 TEPEC, 300059 TEPEC
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| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sean Daugherty |
| E-mail(s) |
sdaugherty@som.umaryland.edu
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| Phone |
410-706-8012
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| Organization name |
University of Maryland School of Medicine
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| Department |
Institute for Genome Sciences
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| Street address |
801 W. Baltimore St.
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21201 |
| Country |
USA |
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| Platform ID |
GPL21006 |
| Series (1) |
| GSE73885 |
Comparative transcriptomics of the virulence regulons of enteropathogenic Escherichia coli from diverse phylogenomic lineages |
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| Relations |
| BioSample |
SAMN02673528 |
| SRA |
SRX481650 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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