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Sample GSM7440463 Query DataSets for GSM7440463
Status Public on Mar 26, 2024
Title CspE CLIP-seq, UV-crosslinked, biol rep 2 (Sample 9)
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-003807
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 SAMN35570967
SRA SRX20578886

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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