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| Status |
Public on May 06, 2024 |
| Title |
NhaC-0M |
| Sample type |
SRA |
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| Source name |
NhaC Na+/H+ antiporter (H2569) -expressed TO114 strain
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| Organism |
Escherichia coli |
| Characteristics |
strain: NhaC Na+/H+ antiporter (H2569) -expressed TO114 strain
treatment: control
time: 4 h
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| Growth protocol |
E. coli cells were cultured at 37ºC in LBK media with 50 μg/ml of ampicillin and 25 μg/ml of kanamycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted utilizing TRIzol LS Reagent (Thermo Fisher Scientific), according to the manufacturer’s protocol.
RNA samples were utilized to construct the libraries, which were sequenced.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated.
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with Bowtie. Transcript abundances are measured with mapped read count within gene region. In case of strand specific library, sense or anti-sense read counts are extracted by strand.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage.
In groups with different conditions, genes or transcripts that express differentially are filtered out through statistical hypothesis testing.
Assembly: Escherichia coli K12- W3110 (https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000110)
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample
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| Submission date |
Apr 23, 2024 |
| Last update date |
May 06, 2024 |
| Contact name |
Hakuto Kageyama |
| E-mail(s) |
kageyama@meijo-u.ac.jp
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| Organization name |
Meijo University
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| Street address |
1-501, Shiogamaguchi, Tempaku-ku
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| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
4688502 |
| Country |
Japan |
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| Platform ID |
GPL25368 |
| Series (1) |
| GSE264731 |
Transcriptome analysis of Escherichia coli TO114 under salt stress |
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| Relations |
| BioSample |
SAMN41064754 |
| SRA |
SRX24349860 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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