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| Status |
Public on Dec 14, 2023 |
| Title |
RNA-seq WT mid-log phase rep 2 |
| Sample type |
SRA |
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| Source name |
Bacteria
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| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 |
| Characteristics |
strain: LT2
medium: glucose M9 minimal
phase: mid-log phase
genotype: wild type
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| Growth protocol |
glycerol stocks of Salmonella enterica serovar Typhimurium strain LT2 were inoculated into M9 minimal media with 0.2% (w/v) glucose. M9 minimal media was also supplemented with 1 ml trace element solution (100X) containing 1 g EDTA, 29 mg ZnSO4.7H2O, 198 mg MnCl2.4H2O, 254 mg CoCl2.6H2O, 13.4 mg CuCl2, and 147 mg CaCl2. The culture was incubated at 37 oC overnight with agitation, and then was used to inoculate the fresh media (1/200 dilution). The volume of the fresh media was 150 mL for each biological replicate. The fresh culture was incubated at 37 oC with agitation to the mid-log phase (OD600 ≈ 0.5).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Three milliliters of the cells cultured up to the exponential phase and 6 ml of RNAprotect Bacteria Reagent (Qiagen) were mixed immediately by vortexing for 5 sec, followed by 5 min incubation at room temperature and, after, centrifuged at 5000x g for 10 min. The supernatant was extracted, but for full supernatant removal the tube was inverted once onto a paper towel. Isolation of total RNA samples was conducted with RNeasy Plus Mini kit (Qiagen). The quantity was determined by Nanodrop 1000 spectrophotometer (Thermo Scientific). The quality was checked using RNA 6000 Pico Kit using Agilent 2100 Bioanalyzer (Agilent). Paired-end, strand-specific RNA-seq library was built with the help of KAPA RNA Hyper Prep kit (Kapa Biosystems)
The RNA libraries were prepared for sequencing based on Illumina standard protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Salmonella enterica serovar Typhimurium LT2 RNA-seq mid-log phase replicate 2
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| Data processing |
The sequencing was performed on HiSeq 2500 (Illumina).
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_003197) using bowtie with 1000 bp as the max. insert size and 2 max. mismatches after cutting 3 bp at 3' ends.
SAM files generated from bowtie, then, were then used for Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM).
Cufflinks was run with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: Salmonella enterica serovar Typhimurium LT2 genome (NC_003197)
Supplementary_files_format_and_content: Tab-delimited text files in gff format which has 8 columns: sequence id, source(empty), feature (+/- strand), start position, end position, intensity score, strand(+/-), frame(.), attribute(.).
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| Submission date |
Sep 14, 2018 |
| Last update date |
Dec 14, 2023 |
| Contact name |
Donghyuk Kim |
| E-mail(s) |
dkim@unist.ac.kr
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| Organization name |
UNIST
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| Department |
Department of Chemical Engineering
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| Lab |
Systems Biology Lab
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| Street address |
50 UNIST-gil, Eonyang-eup, Ulju-gun
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| City |
Ulsan |
| ZIP/Postal code |
44919 |
| Country |
South Korea |
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| Platform ID |
GPL22503 |
| Series (2) |
| GSE119966 |
Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution (RNA-seq) |
| GSE119967 |
Experimental promoter identification of a representative food-borne pathogen Salmonella enterica serovar Typhimurium LT2 with near single base-pair resolution |
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| Relations |
| BioSample |
SAMN10060567 |
| SRA |
SRX4680595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3389571_Salmonella_typhimurium_LT2_RNA-seq_exp2.gff.gz |
31.8 Mb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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