|
| Status |
Public on Dec 31, 2016 |
| Title |
hns_2 |
| Sample type |
SRA |
| |
|
| Source name |
Enterohemorrhagic Escherichia coli O157:H7 strain EDL933
|
| Organism |
Escherichia coli O157:H7 str. EDL933 |
| Characteristics |
genotype: {delta}hns
phase: logarithmic phase
|
| Treatment protocol |
The bacteria were centrifuged at 4000×g at 4°C for 5 min and then washed with PBS.
|
| Growth protocol |
Overnight cultures of bacteria were diluted 1:100 in fresh LB broth and grown to logarithmic phase at an OD600 of about 0.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using RiboPure-BacteriaTM Bacteria kit according to the manufacturer's protocol (Ambion, Life Technologies). DNase I treatment was applied to eliminate genomic DNA contamination as per the manufacturer's recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
All raw FastQ files generated were filtered using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads per kilobase of exon model per million mapped reads (RPKM) was used as a normalized metric to present the gene expression levels.(Nature methods 2008, 5: 621-628)
Transcripts evaluation of differential expression were accomplished using MARS (MA-plot-based method with Random sampling model) in DEGseq package.(Bioinformatics 2010, 26: 136-138)
Genome_build: NC_002655.2
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Baoshan Wan |
| E-mail(s) |
[email protected]
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
Laboratory of Bacterial Pathogenesis
|
| Street address |
Rm 710, Bldg 5, 280 S. Chongqing Rd
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL21021 |
| Series (1) |
| GSE73969 |
RNA-seq to profile the H-NS transcriptome in EHEC O157:H7 strain EDL933 |
|
| Relations |
| BioSample |
SAMN04161021 |
| SRA |
SRX1331712 |
