|
| Status |
Public on Mar 26, 2024 |
| Title |
CspE CLIP-seq, UV-crosslinked, biol rep 3 (Sample 11) |
| Sample type |
SRA |
| |
|
| Source name |
SL1344
|
| Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
| Characteristics |
strain: SL1344
genotype: cspE-3xFLAG
treatment: UV-crosslinked
rip antibody: anti-FLAG
|
| Treatment protocol |
One half of the culture was irradiated with UV-C light at 800 mJ to induce RBP crosslinking. Bacteria were lysed and the FLAG-tagged protein was immunoprecipitated using a monoclonal anti-FLAG antibody.
|
| Growth protocol |
Overnight growth from single colonies at 37 °C in LB medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phase-lock tubes (5PRIME) were used to mix 450 µl of Phenol:Chloroform:Isoamyl alcohol 25:24:1 (PCI; Roth) with the supernatant from proteinase K treated samples (around 450 µl).
cDNA libraries were prepared using the NEBnext Multiplex Small RNA library kit (#E7300) according to the manufacturer’s recommendation.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ID-003809
cspE_CLIP_peaks.gff
CspE_counts.csv
|
| Data processing |
PCR duplicates were removed using FastUniq v1.1 (Xu et al. 2012)
Adapters were removed with Cutadapt v4.1, read length 12-25
Alignment: segemehl 0.3.4
Peak Calling: blockbuster 0.0.1.1
Adapters were removed with Cutadapt v4.1, no upper limit on read length, min. read length 12
Alignment: STAR 2.6.0a (Dobin et al., 2013)
Quantification of peaks: htseq-count 2.0.2
Assembly: FQ312003.1, HE654724.1, HE654725.1 and HE654726.1
Supplementary files format and content: Quantification of peaks
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Laura Jenniches |
| E-mail(s) |
laura.jenniches@helmholtz-hiri.de
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Street address |
Josef-Schneider-Straße 2/D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21220 |
| Series (2) |
| GSE234007 |
Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [CLIP-seq] |
| GSE234010 |
Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives |
|
| Relations |
| BioSample |
SAMN35570965 |
| SRA |
SRX20578888 |
