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Sample GSM7918660 Query DataSets for GSM7918660
Status Public on Mar 04, 2024
Title EPIC-1 DC
Sample type SRA
 
Source name N/A
Organism synthetic construct
Characteristics cell line: N/A
sample type: in vitro cDNA
treatment: EPIC-1 DC samples suspended in a denaturing buffer containing formamide and incubated at 95 °C prior to modification with NAI
Treatment protocol For in vitro SHAPE-MaP, 50-200 ng RNAs were obtained under each treatment, and then used for SHAPE-MaP reverse transcription by adding 1 uL (200 U/uL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for EPIC. Mn2+ was removed using RNAClean XP (Beckman Coulter) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.
Growth protocol NA
Extracted molecule other
Extraction protocol For in vitro SHAPE-MaP, RNA are purified. About 50-200 ng of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for EPIC. Mn2+ was removed using RNAClean XP (Beckman Coulter) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase.
circSHAPE-MaP libraries were prepared from 1 ng DNAs for circular RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Library was prepared by KAPA Hyper Prep Kit. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NovaSeq.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description EPIC_1_DC
Data processing *library strategy: circSHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to experimental barcodes.
Analyses by CIRCshapemapper v2 (https://github.com/YangLab/circSHAPEmapper)
Assembly: Target RNA sequence
Supplementary files format and content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.
 
Submission date Nov 27, 2023
Last update date Mar 06, 2024
Contact name Li Yang
E-mail(s) liyang_fudan@fudan.edu.cn
Organization name Fudan University
Department Institutes of Biological Sciences
Street address 131 Dong-An Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL26526
Series (2)
GSE248679 circSHAPE-MaP of EPIC
GSE248680 Therapeutic application of circular RNA aptamers in a mouse model of psoriasis
Relations
BioSample SAMN38450781
SRA SRX22651853

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

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