|
| Status |
Public on Sep 28, 2022 |
| Title |
pNM-MS2_elute_1 |
| Sample type |
SRA |
| |
|
| Source name |
MG1655
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
strain: MG1655
plasmid: pBR-lacI-MS2
pulldown sample type: Eluate
|
| Treatment protocol |
Cells were harvested by centrifugation, and cell pellets were snap frozen in liquid nitrogen.
|
| Growth protocol |
Bacterial strains were grown shaking at 250 rpm at 37˚C in Gutnick medium supplemented with HoLE, 0.4% glucose, 15 mM ammonium, and ampicillin, and samples were collected at stationary phase (9 hours of growth).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard TRIzol protocol was used for 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 |
| |
|
| Description |
RNA sequencing library after MAPS pulldown performed with control MS2 vector - Replicate 1
|
| Data processing |
fastq records trimming (cutadapt 3.0)
short reads mapping (rilseq 0.60)
read counting (featureCounts/2.0.2)
Assembly: ecoli-k12-MG1655-NC_000913-3
Supplementary files format and content: Read counts in tab-delimited text file
|
| |
|
| Submission date |
Mar 31, 2022 |
| Last update date |
Mar 16, 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) |
| GSE199845 |
A 3´ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria |
|
| Relations |
| BioSample |
SAMN27121266 |
| SRA |
SRX14685797 |
