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| Status |
Public on Nov 15, 2021 |
| Title |
CY1102-2 |
| Sample type |
SRA |
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| Source name |
E. coli CY1102
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| Organism |
Escherichia coli |
| Characteristics |
strain: CY1102
genotype: clpX-V78F (manipulated)
culture conditions: Batch culture at 37oC, OD600~0.4
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| Treatment protocol |
No treatment.
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| Growth protocol |
In N-C- minimal medium supplemented with 22 mM glucose, 20 mM NH4Cl, and 0.2% (w/v) Casamino acid aerobically at 37°C water bath, 250rpm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
All samples were quick freezed in liquid nitrogen and stored at -80 °C for RNA extraction. Total RNA was extracted by RNAiso plus (Takara) and PureLink RNA Mini Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
1st-round RNA-Seq Assays
CY1102.txt
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, poly-N and low-quality sequence, then mapped to NCM3722 whole genome using bowtie2 v2.2.3 with parameters -q --phred33 --sensitive -I 100 -X 500 --end-to-end --no-unal -p 4.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. To avoid counting reads from the neighbor genes, we use TMM to normalize the read count.
Genome_build: NCM3722 (NZ_CP011495.1 and NZ_CP011496.1)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample.
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| Submission date |
Jan 19, 2021 |
| Last update date |
Nov 15, 2021 |
| Contact name |
Conghui You |
| E-mail(s) |
[email protected]
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| Organization name |
Shenzhen University
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| Street address |
1068 Xueyuan Rd., Nanshan District
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| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518037 |
| Country |
China |
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| Platform ID |
GPL25368 |
| Series (1) |
| GSE165151 |
The strategy of a novel way to enhance bacterial motility |
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| Relations |
| BioSample |
SAMN17385895 |
| SRA |
SRX9899707 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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