|
| Status |
Public on Apr 21, 2021 |
| Title |
stationary_minus_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
E. coli K-12 stain MG1655
|
| Organism |
Escherichia coli |
| Characteristics |
tissue: E. coli K-12 stain MG1655
phase: stationary minus
|
| Growth protocol |
grown in Luria-Bertani (LB) broth under aeration at 37 °C to an OD600 of 1.9
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted according to the method described by Winz et al, 2017
For each RNA sample, 1 μg poly(A)-tailed RNA was used to prepare a library using the Nanopore Direct RNA Sequencing Kit (RNA-0002) following the manufacturer’s instructions (Oxford Nanopore Technologies, Oxford, UK). Each library was loaded onto a flow cell (R9.4) and sequenced on the sequencing device GridION.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
GridION |
| |
|
| Data processing |
The bioinformatic analysis was conducted using our home-made pipeline, TagSeqTools36. Tagged and non-tagged reads were differentiated using the TagSeek module with default setting (similarity=12). Two sets of reads generated from the TagSeek step were subjected to TagSeqQuant for alignment to both the reference genome and transcriptome of E. coli strain K-12 substrain MG165537, with the default alignment parameters of minimap2
Genome_build: E. coli strain K-12 substrain MG1655
Supplementary_files_format_and_content: excel files including comparisons between different samples
|
| |
|
| Submission date |
Jun 25, 2020 |
| Last update date |
Apr 21, 2021 |
| Contact name |
Huan ZHONG |
| E-mail(s) |
zhdorothy5@gmail.com
|
| Phone |
91493987
|
| Organization name |
HKBU
|
| Department |
BIOLOGY
|
| Street address |
T1012 CHA CHI-MING SCIENCE TOWER
|
| City |
HONG KONG |
| State/province |
HONG KONG |
| ZIP/Postal code |
00000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL28771 |
| Series (1) |
| GSE153253 |
NAD+-capped RNAs are preferentially produced from inducible genes in response to growth conditions in E. coli |
|
| Relations |
| BioSample |
SAMN15368624 |
| SRA |
SRX8616699 |
