|
| Status |
Public on Jul 01, 2016 |
| Title |
MT2 |
| Sample type |
SRA |
| |
|
| Source name |
10403s null nmlR strain
|
| Organism |
Listeria monocytogenes 10403S |
| Characteristics |
genotype/variation: null nmlR
|
| Growth protocol |
L. monocytogenes strains were grown until early stationary phase. Early stationary phase is defined as a culture incubated at 37C with 200 rpm agitation until OD 600 reached 1.0 with 3 additional hours of incubation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained by Ribopure RNA extraction kit (Ambion). rRNA in RNA samples was depleted by MICROBExpress bacterial mRNA enrichment kit.
The whole transcriptome library was constructed by Ion total RNAseq kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
rRNA depleted RNA
|
| Data processing |
.sff file from Ion torrent machine was converted to fastq file by sff2fastq code.
FastQC program was obtained to determine quality of output sequences.
GetSpecificLengthRead.cpp was used to trim the sequences before alignment.
EDGE-pro was obtained to align the sequences to 10403s reference genome and to detemine differentially expressed genes between the two stains of L. monocytogenes.
RPKM data from EDGE-pro were compared and sorted in Microsoft Excel.
Genome_build: NC_017544.1 (ASM16869v2)
Supplementary_files_format_and_content: RPKM values for each sample
|
| |
|
| Submission date |
Jun 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sirirak Supa-amornkul |
| E-mail(s) |
[email protected]
|
| Organization name |
Mahidol University
|
| Department |
Microbiology
|
| Street address |
272 Payatai
|
| City |
bangkok |
| ZIP/Postal code |
10400 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL20617 |
| Series (1) |
| GSE70265 |
Transcriptomic and phenotypic studies of Listeria monocytogenes NmlR in stress response |
|
| Relations |
| BioSample |
SAMN03794781 |
| SRA |
SRX1073167 |
