NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8244045 Query DataSets for GSM8244045
Status Public on May 06, 2024
Title Natural and artificial sequences, 1M7 treated sample, 5mM Mg, 0,1mM SAM, replicate 1
Sample type SRA
 
Source name bacteria
Organism Bacteria
Characteristics cell type: bacteria
Treatment protocol N/A
Growth protocol N/A
Extracted molecule other
Extraction protocol N/A
RNAs were in vitro transcribed, modified with SHAPE reagent and reverse transcribed with the Superscript III reverse transcriptase (Invitrogen®) and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs®) as manufacter’s instructions.
 
Library strategy RNA-Seq
Library source other
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Multiple bacterial species (RFAM RF00162)
dsDNA library, 206 SAM-I aptamer natural sequences and 100 Artificial sequences
Data processing The demultiplexing is made using cutadapt. (https://cutadapt.readthedocs.io/en/stable/)
Quality trimming, Paired read merging, Sequence alignment, Mutation identification, Mutation counting, Sequence correction, reactivity profile calculation were made by using Shapemapper 2 (https://github.com/Weeks-UNC/shapemapper2)
Assembly: N/A
Supplementary files format and content: Tab-separated values files
 
Submission date Apr 30, 2024
Last update date May 06, 2024
Contact name Pierre HARDOUIN
E-mail(s) pierre.hardou@gmail.com
Phone 0676574883
Organization name Faculté de pharmacie UMR 8038
Department CiTCoM
Lab MÉCANISMES MOLÉCULAIRES DE LA TRADUCTION DE L’ARN VIRAL
Street address 4 avenue de l'observatoire
City Paris
State/province France
ZIP/Postal code 75006
Country France
 
Platform ID GPL34432
Series (1)
GSE266263 Designing Molecular RNA Switches with Restricted Boltzmann Machines
Relations
BioSample SAMN41144246
SRA SRX24416787

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap