|
| Status |
Public on Sep 26, 2023 |
| Title |
pZE_2_control for pZE-FliX |
| Sample type |
SRA |
| |
|
| Source name |
MG1655(crl-) + pZE
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
cell type: Escherichia coli K-12
genotype/variation: Control library of pZE-FliX
growth: OD ~ 0.2
|
| Treatment protocol |
Cells were harvested by centrifugation, washed with 1X PBS, and cell pellets snap frozen by liquid nitrogen.
|
| Growth protocol |
Bacterial strains were grown at 37˚C , shaking at 250 rpm, in LB rich medium and samples were collected at OD~0.2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard TRIzol protocol was used for total RNA extraction.
Library construction was carried out based on the RNAtag-Seq methodology (Shishkin et al., 2015), which was adapted to capture bacterial sRNAs (Melamed et al., 2018)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastq records trimming (cutadapt 3.7)
short reads mapping (rilseq 0.74)
wiggle file generation (deeptools 3.5.1)
Supplementary files format and content: wiggle file
|
| |
|
| Submission date |
Dec 12, 2022 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Ryan Dale |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute of Child Health and Human Development
|
| Lab |
Bioinformatics and Scientific Programming Core
|
| Street address |
Rm 10D39, 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24570 |
| Series (1) |
| GSE174487 |
Sigma 28-dependent small RNAs regulate timing of flagella biosynthesis |
|
| Relations |
| BioSample |
SAMN32173633 |
| SRA |
SRX18653887 |
