|
| Status |
Public on Dec 08, 2019 |
| Title |
Wild type strain RNA-Seq 3_wt 3 |
| Sample type |
SRA |
| |
|
| Source name |
MG1655
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
growth: Subcultured for 150 min in LB
|
| 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 either LB rich or M63 minimal medium and samples were collected at OD~1 in experiments 1 and 3, and at 150 min in experiment 2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard TRIzol protocol was used for total RNA extraction and standard TRI Reagent LS protocol was used for RNA extraction in the RIL-seq protocol
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)
RIL-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Wild type strain
total RNA
Total RNA library_exp3
|
| Data processing |
fastq records trimming (cutadapt 1.16)
short reads mapping and wiggle file generation (rilseq 0.60)
chimera mapping and s-chimera reporting (rilseq 0.60)
BED file genreration (rilseq 0.60)
Genome_build: ecoli-k12-MG1655-NC_000913-3
Supplementary_files_format_and_content: BED format for significant chimeric fragments of RILseq samples.
Supplementary_files_format_and_content: Wiggle format for RNAseq samples
|
| |
|
| Submission date |
May 20, 2019 |
| 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) |
| GSE131520 |
RNA-RNA interactomes of Hfq and ProQ reveal overlapping and competing roles for RNA chaperones |
|
| Relations |
| BioSample |
SAMN11788390 |
| SRA |
SRX5871067 |
