|
| Status |
Public on Nov 17, 2020 |
| Title |
SPI1_RBP1 |
| Sample type |
SRA |
| |
|
| Source name |
SPI1 RBP1
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 |
| Characteristics |
sample type: LB broth OD 2.0 SPI1-inducing
|
| Treatment protocol |
Cultures were not treated with chloramphenicol and harvested by rapid filtration/chilling
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see molecule, above
sRNA protocol for Illumina Nextseq500
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribosome mRNA footprints, ribosomes and footprints created by MNase digestions were harvested and size-selected (26-34 nt)
|
| Data processing |
Basecalling with RTA 2.4.11
Trimming performed with cutadapt 2.1 (HRIBO 1.4.3)
rRNA filtering with samtools 1.9 (HRIBO 1.4.3)
Mapping with segemehl 3.4 (HRIBO 1.4.3)
Coverage file creation with HRIBO 1.4.3
Genome_build: ASM21085v2
Supplementary_files_format_and_content: wig files were generated with single nucleotide mapping and converted to bigwig
|
| |
|
| Submission date |
May 05, 2020 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Florian Eggenhofer |
| Organization name |
University of Freiburg
|
| Department |
Institute for Informatics
|
| Lab |
Chair for Bioinformatics
|
| Street address |
Georges Köhler Allee 106
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL20056 |
| Series (1) |
| GSE149893 |
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence |
|
| Relations |
| BioSample |
SAMN14836467 |
| SRA |
SRX8249101 |
