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| Status |
Public on Jun 01, 2022 |
| Title |
Methanol rep1 |
| Sample type |
SRA |
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| Source name |
Bacterial culture with methanol
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| Organism |
Escherichia coli |
| Characteristics |
strain: Escherichia coli str. K-12 substr. MG1655
genotype: wild type
conditions: 2% (v/v) methanol
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| Growth protocol |
E. coli K-12 MG1655 was incubated in 3 ml LB liquid for 14 h at 37℃ with constant shaking, and then 10 uM toxoflavin and 100 uM tropolone dissolved in methanol were added to each culture. Additional incubation was performed for 2 h.
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| Extracted molecule |
total RNA |
| Extraction protocol |
After 2 h of the treatment, 1 ml of each culture centrifuged and total RNA was prepared using RNeasy Midi kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocols. A MICOBExpressTM bacterial mRNA enrichment kit (Ambion, Austin, TX, USA) was used to remove bacterial rRNA from the total RNA samples.
Nine libraries for RNA-seq were prepared using the Illumina TruSeqTM RNA sample prep kit with the standard low-throughput protocol. Sequencing was performed on an Illumina HiSeq2000 instrument.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Using FASTX-Toolkit, raw data derived from RNA-seq was filtered to a minimum phred quality score of 28.
The BWA-MEM algorithm was employed to align the filtered reads into the reference genome.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by featureCounts tool in the Subread package.
Counted values were nomalised in the RPKM method.
Genome_build: Escherichia coli K-12 MG1655 GCF_000005845.2
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jun 26, 2019 |
| Last update date |
Jun 01, 2022 |
| Contact name |
Jungwook Park |
| E-mail(s) |
jjuwoogi@pusan.ac.kr
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| Organization name |
Pusan National University
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| Department |
Microbiology
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| Street address |
Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea
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| City |
Busan |
| ZIP/Postal code |
ASI|KR|KS012|PUSAN |
| Country |
South Korea |
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| Platform ID |
GPL14548 |
| Series (1) |
| GSE133348 |
Transcriptome analysis of Escherichia coli K-12 MG1655 under toxoflavin and troplone conditions |
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| Relations |
| BioSample |
SAMN12142315 |
| SRA |
SRX6367805 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3906079_Methanol_1.txt.gz |
87.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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