|
| Status |
Public on Mar 04, 2024 |
| Title |
EPIC-PKR NAI,repeat1 |
| Sample type |
SRA |
| |
|
| Source name |
N/A
|
| Organism |
synthetic construct |
| Characteristics |
cell line: N/A
sample type: in vitro cDNA
treatment: EPIC-PKR NAI samples modified by NAI in DMSO
|
| 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_PKR_NAI_rep1
|
| 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 |
SAMN38450777 |
| SRA |
SRX22651857 |
