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Status |
Public on Mar 04, 2024 |
Title |
EPIC-2 DMSO |
Sample type |
SRA |
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Source name |
N/A
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Organism |
synthetic construct |
Characteristics |
cell line: N/A sample type: in vitro cDNA treatment: EPIC-2/EPIC-PKR DMSO samples only treated with DMSO
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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.
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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.
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Library strategy |
OTHER |
Library source |
other |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
EPIC_2_DMSO
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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.
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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 |
SAMN38450774 |
SRA |
SRX22651860 |