|
| Status |
Public on Dec 18, 2023 |
| Title |
DC_pre_ANKRD52_DNAtemplate |
| Sample type |
SRA |
| |
|
| Source name |
PA1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: PA1
treatment: pre_ANKRD52 with DNA template DC samples denatured by formamide at 95C
|
| Treatment protocol |
In vitro synthesized circular or linear ankrd52 RNAs were incubated with or without an equal amount of DNA template respectively, heated for 5 min at 65 ℃ in PA buffer (10 mM Tris pH 7.5, 10 mM MgCl2, 100 mM NH4Cl) and slowly cooled down to room temperature in vitro. The mixture was then treated with DMSO or SHAPE reagent NAI at a final concentration of 200 mM respectively and incubated at 37 ℃ for 15 min. Meanwhile, in vitro synthesized circular or linear ankrd52 RNAs were heated for 1 min at 95 ℃ with denaturing buffer (60% formamide, 20 mM HEPES PH 8.0, 1.6 mM EDTA PH 8.0), and instantly cooled down to denature RNAs. The denatured RNAs were labeled with NAI at a final concentration of 200 mM at 95 ℃ for 1 min as denaturing control (DC).
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs in the reactions were extracted by TRIZOL according to the manufacturer’s protocol, followed by DNase I digestion and phenol/chloroform extraction.
Next, recovered RNAs were used for reverse transcription using SuperScript II (Invitrogen) and specific primers for circular or linear ankrd52 RNAs. Finally, nest PCRs were done to amplify circular or linear ankrd52 DNAs using primers for library preparation and deep sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Analyses by Shapemapper V2.1.3.
Genome_build: 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 |
Sep 10, 2021 |
| Last update date |
Dec 18, 2023 |
| 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 |
GPL20795 |
| Series (2) |
| GSE183927 |
ANKRD52_SHAPE-MaP |
| GSE183930 |
Linking circular intronic RNA degradation and function in transcription by RNase H1 |
|
| Relations |
| BioSample |
SAMN21386878 |
| SRA |
SRX12136079 |
