 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 15, 2021 |
| Title |
CY598-1 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli CY598
|
| Organism |
Escherichia coli |
| Characteristics |
strain: CY598
genotype: Wild Type
culture conditions: Batch culture at 37oC, OD600~0.4
|
| Treatment protocol |
No treatment.
|
| 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.
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
1st-round RNA-Seq Assays
CY598-round1.txt
|
| 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.
|
| |
|
| Submission date |
Jan 19, 2021 |
| Last update date |
Nov 15, 2021 |
| Contact name |
Conghui You |
| E-mail(s) |
[email protected]
|
| Organization name |
Shenzhen University
|
| Street address |
1068 Xueyuan Rd., Nanshan District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518037 |
| Country |
China |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE165151 |
The strategy of a novel way to enhance bacterial motility |
|
| Relations |
| BioSample |
SAMN17385902 |
| SRA |
SRX9899700 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
