|
| Status |
Public on Jul 22, 2022 |
| Title |
STEC_CW |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Escherichia coli |
| Characteristics |
sample type: Shiga toxin-producing Escherichia coli
strain: 86-24
treatment: Incubation with supernatant from Citrobacter werkmanii culture
|
| Treatment protocol |
STEC and EAEC were centrifuged at 5000 rpm for 10 min. The supernatant was removed and the pellet was resuspended with M9 media (control), supernatant from Citrobacter werkmanii (CW) or supernatant from Escherichia albertii (EA) and incubated for 3 h at 37 ºC and 150 rpm
|
| Growth protocol |
STEC and EAEC overnight culture were diluted 1/50 in DMEM media and left to grow for ~3 h at 37 ºC and 180 rpm, until bacteria reached an OD600 equal to 0.3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent
RNA libraries were prepared using Ribo-Zero rRNA Removal Kit (Bacteria) and TruSeq Stranded Total RNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of the sequenced raw reads were analyzed with FastQC v0.11.5
Low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates were removed, using Trimmomatic v0.32
Trimmed reads were mapped to Escherichia coli 042 or Escherichia coli strain NADC 5570/86-24/6564 reference genome with Bowtie v1.1.2
HTseq v0.6.1p1 was used for expression profiling. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand. Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) value or the RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value
DEG (Differentially Expressed Genes) analysis was performed on a 2 comparisons pairs using RPKM.
Genome_build: ASM180628v1 (Escherichia coli strain NADC 5570/86-24/6564)
Genome_build: ASM2712v1 (Escherichia coli 042)
Supplementary_files_format_and_content: tab-delimited text files include counts values for each gene in sample
Supplementary_files_format_and_content: GFF (General Feature Format) files including gene annotation for STEC or EAEC
|
| |
|
| Submission date |
Mar 02, 2022 |
| Last update date |
Jul 24, 2022 |
| Contact name |
Mauricio J. Farfan |
| E-mail(s) |
[email protected]
|
| Organization name |
Universidad de Chile
|
| Department |
Departamento de Pediatria y Cirugia Infantil
|
| Street address |
Antonio Varas 360, Providencia
|
| City |
Santiago |
| ZIP/Postal code |
7500539 |
| Country |
Chile |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE197797 |
Bacteria from gut microbiota associated with diarrheal infections in children promote virulence of Shiga toxin-producing and enteroaggregative Escherichia coli pathotypes. |
|
| Relations |
| BioSample |
SAMN26367215 |
| SRA |
SRX14354079 |
