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Sample GSM4728909 Query DataSets for GSM4728909
Status Public on Aug 17, 2020
Title Aptamer21-PEARL-DMSO-Cmpd2a-S-None-1
Sample type SRA
 
Source name In vitro transcription
Organism Synthetic plasmid
Characteristics library type: PEARL-seq
scale: Targeted
platform: MiSeq
Extracted molecule total RNA
Extraction protocol All Aptamer 21 derivatives were produced by in vitro transcription (IVT) from linearized plasmid templates, using the HiScribe IVT kit (New England Biolabs) according to the manufacturer’s standard protocol with 33.5 ng/µL template. Total RNA was extracted from 12 samples of 2x10^5 to 1.5x10^6 HepG2 cells using the ReliaPrep RNA cell miniprep system (Promega) according to the manufacturer’s standard protocol.
Libraries were produced using standard Illumina protocols.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiSeq
 
Data processing Reads were stitched with Paired-End reAd mergeR (PEAR) requiring a minimum assembled length of at least 10 nucleotides (nt)
PEARL-seq reads were trimmed with Cutadapt (at least 5-nt of overlap and a maximum of 20% mismatches), DMS-MaP and SHAPE-MaP reads were trimmed with Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Targeted experiment reads were aligned with Bowtie2. Transcriptome-wide experiments were aligned with STAR
Mutation rates (MaP) and RT stalls (PEARL-seq) were called using an in-house pipeline (https://bitbucket.org/arrakistx/pearl-seq/src/master/)
Genome_build: hg38 + Aptamer21 spikein
Supplementary_files_format_and_content: *_mut_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC, Reactivity
Supplementary_files_format_and_content: *_stall_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC
Supplementary_files_format_and_content: *_10ntBinCounts.txt (Transcriptome-wide experiments only) tabulating stalls across genomic 10nt bins. 0-count bins are not reported
 
Submission date Aug 16, 2020
Last update date Aug 17, 2020
Contact name Lee Vandivier
E-mail(s) lvandivier@arrakistx.com
Phone 7816849777
Organization name Arrakis Therapeutics
Street address 830 Winter St
City Waltham
State/province MA
ZIP/Postal code 02451
Country USA
 
Platform ID GPL20106
Series (1)
GSE156312 PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions
Relations
BioSample SAMN15828988
SRA SRX8953286

Supplementary file Size Download File type/resource
GSM4728909_Aptamer21-PEARL-DMSO-Cmpd2a-S-None-1-agg_stall_rate.txt.gz 3.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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