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Sample GSM7892991 Query DataSets for GSM7892991
Status Public on Nov 14, 2023
Title A-DMSO
Sample type SRA
 
Source name Synthesized A RNA library
Organism synthetic construct
Characteristics tissue: Synthesized A RNA library
treatment: DMSO
Treatment protocol A-case/U-case RNA libraries were probed with 50mM (S,R) 1/ 100uM (S,R) 2/ DMSO at 0℃ for 2h
Extracted molecule other
Extraction protocol RNAs were purified by washing with Rnase-free water using centrifuge filters after probing
RNAs were all folded independently before mixing to build a library; and the mixing was done immediately before probing
 
Library strategy OTHER
Library source other
Library selection other
Instrument model HiSeq X Ten
 
Data processing Sequencing reads were processed by previouly established icSHAPE pipine (https://github.com/qczhang/icSHAPE).
Data was first demultiplexed, removed PCR dplicates and trimmed by using the scripts of icSHAPE pipeline.
Read quality was checked for each sample using FastQ v0.11.9
High-quality reads were then imported into bowtie2 v2.4.5 for alignment into BAM files.
BAM files were imported into the icSHAPE pipelineto calucate the RPKM and RT-stops frequency.
Assembly: Alignment was to the designed A/U RNA library sequences built from solid-phase synthesis.
Supplementary files format and content: excel (.xlsx); containingR-score of each samples calculated by RT-stop frequency per nucleotide.
 
Submission date Nov 13, 2023
Last update date Nov 14, 2023
Contact name Lu Xiao
E-mail(s) luxiao@stanford.edu
Organization name Stanford University
Street address 369 N-S Axis, Stauffer I, 109
City Stanford
State/province California
ZIP/Postal code 94305
Country USA
 
Platform ID GPL26697
Series (1)
GSE247565 Stereoselective RNA Reaction with Chiral 2'-OH Acylating Agents
Relations
BioSample SAMN38224765
SRA SRX22501546

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

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