|
| Status |
Public on Oct 04, 2021 |
| Title |
CFSCsakATCC29544LEP1_RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Cronobacter sakazakii ATCCTM29544
|
| Organism |
Cronobacter sakazakii |
| Characteristics |
tissue: Bacterial cell
strain: ATCCTM29544
growth stage: LEP
treatment: Static growth at 25 degrees C until LEP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNeasy Mini Kit (Qiagen, USA)
Commercial Illumina RNA-seq library preparation protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw sequence reads were mapped against the C. sakazakii ATCCTM29544 complete genome (NCBI GenBank accession number CP011047) using Segemehl with mapping accuracy set at 100%
Expression values of each gene were calculated using the transcript per million (TPM) method
Annotation of the transcriptomic data was carried out based on PATRICK database (version 3.4.5) and BLAST
Gene expression level alterations larger than 4-fold, between 2- and 4-fold, between 2- and 0.5-fold-, between 0.25- and 0.5-fold and smaller than 0.25-fold respectively defined as highly-up regulated, up regulated, no change, down regulate and highly-down regulated
Genome_build: CP011047
Supplementary_files_format_and_content: text file with TPM
|
| |
|
| Submission date |
Apr 09, 2019 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Yu Cao |
| Organization name |
University College Dublin
|
| Street address |
University College Dublin, Belfield, Dublin 4
|
| City |
Dublin |
| ZIP/Postal code |
04 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL26479 |
| Series (1) |
| GSE129553 |
RNA-seq of desiccated Cronobacter sakazakii ATCCTM29544 on stainless steel coupons |
|
| Relations |
| BioSample |
SAMN11380125 |
| SRA |
SRX5659294 |
