|
Status |
Public on Mar 26, 2024 |
Title |
CspC CLIP-seq, not UV-crosslinked, biol rep 1 (Sample 2) |
Sample type |
SRA |
|
|
Source name |
SL1344
|
Organism |
Salmonella enterica subsp. enterica serovar Typhimurium |
Characteristics |
strain: SL1344 genotype: cspC-3xFLAG treatment: Not 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.
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|
Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
ID-003800 cspC_CLIP_peaks.gff CspC_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
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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 |
SAMN35570974 |
SRA |
SRX20578879 |