|
| Status |
Public on Oct 19, 2022 |
| Title |
WT_2DG_1 |
| Sample type |
SRA |
| |
|
| Source name |
14028S
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
bacteria status: WT
2-dg status: with 2-DG
replicate: 1
|
| Growth protocol |
Cultures of WT ∆manZ S.Tm strains were grown in Luria-Bertani (LB) medium at 37 °C shaken for 16h (overnight culture). Cells were washed and diluted to OD 600 of 0.005 in 3ml acidic minimal medium low in phosphate and magnesium (LPM) untreated or treated with 1mM 2-DG (Sigma D8375-5G) and were grown for 16h at 37°C with shaking
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacterial pellets were washed with PBS and resuspended in RLT buffer. Pellets were freeze and thawed for efficient cell lysis and RNA was extracted using the RNeasy mini kit (QIAGEN) with DNase I-treatment (45 minutes at 23°C) (QIAGEN).
RNAtag-seq cDNA libraries was done as previously described in Avraham et al (2016) (Avraham et al., 2016). Bacterial rRNA was depleted using the RiboZero Gold (Bacteria) kit (Illumina) according to the manufacturer’s guidelines. Strand-specific cDNA libraries were prepared and sequenced as Paired-end (R1: 30, R2: 50) using Miniseq machine and 300 mid output kit with total coverage of ~10.5M and mean of ~380K reads per library, ranges from ~35K to ~1.3M. For each condition, biological triplicates were analyzed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiniSeq |
| |
|
| Data processing |
Fastq reads were demultiplex to their respective sample by using fastq-multx (version 1.3.1) and aligned to a composite genome of S.Tm 14028S and mouse (mm10) using STAR (version 2.5.3a).
For S.Tm read counts, R2 reads were calculated by HTSeq.
Data of each organism was normalized to a library size factor. Factors were calculated by dividing the total number of reads from each sample to the median of the total number of reads across all samples.
Data was transformed to log scale after DESeq2 normalization.
Genome_build: composite genome of S.Tm 14028S and mouse (mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalized number of reads (log scale) for each sample
|
| |
|
| Submission date |
Oct 21, 2019 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Roi Avraham |
| E-mail(s) |
roi.avraham@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Street address |
Herzl St 234
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL27640 |
| Series (2) |
| GSE139206 |
Host metabolic reprogramming during immune activation promotes intracellular bacterial survival (2DG) |
| GSE139208 |
Host succinate is a signal for activation of Salmonella virulence during intracellular infection |
|
| Relations |
| BioSample |
SAMN13071312 |
| SRA |
SRX7031446 |
