|
| Status |
Public on Jun 01, 2023 |
| Title |
sor405_3 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli
|
| Organism |
Escherichia coli |
| Characteristics |
strain: CY405
culture method: batch culture at 37C
optical density (od600): approximately 0.4
treatment: none
genotype: delta_fur
|
| Treatment protocol |
add 0.001g/L Ammonium ferric citrate(Fe)
|
| Growth protocol |
in N-C- minimal medium supplemented with 20 mM sorbitol and 20 mM NH4Cl 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 extract 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 |
Batch culture at 37°C, OD600≈0.4
sor405.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: Tab-delimited text files with raw gene counts and RPKM values for every gene and every sample
|
| |
|
| Submission date |
Jun 01, 2021 |
| Last update date |
Jun 01, 2023 |
| Contact name |
Conghui You |
| E-mail(s) |
[email protected]
|
| Organization name |
Shenzhen University
|
| Street address |
1068 Xueyuan Blvd.
|
| City |
Shenzhen |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE175957 |
Exploring Fur regulon in Escherichia coli |
|
| Relations |
| BioSample |
SAMN19490401 |
| SRA |
SRX11042368 |
