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| Status |
Public on Aug 17, 2020 |
| Title |
Aptamer21-PEARL-DMSO-Cmpd2d-None-3 |
| Sample type |
SRA |
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| Source name |
In vitro transcription
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| Organism |
Synthetic plasmid |
| Characteristics |
library type: PEARL-seq
scale: Targeted
platform: MiSeq
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| 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.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| 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
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| Submission date |
Aug 16, 2020 |
| Last update date |
Aug 17, 2020 |
| Contact name |
Lee Vandivier |
| E-mail(s) |
lvandivier@arrakistx.com
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| Phone |
7816849777
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| Organization name |
Arrakis Therapeutics
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| Street address |
830 Winter St
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| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02451 |
| Country |
USA |
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| Platform ID |
GPL20106 |
| Series (1) |
| GSE156312 |
PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions |
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| Relations |
| BioSample |
SAMN15828917 |
| SRA |
SRX8953303 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4728926_Aptamer21-PEARL-DMSO-Cmpd2d-None-3-agg_stall_rate.txt.gz |
3.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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