|
| Status |
Public on Jun 23, 2021 |
| Title |
Ad3(AG)_DC_8mM |
| Sample type |
SRA |
| |
|
| Source name |
In vitro transcribed from plasmid
|
| Organism |
Human adenovirus 2 |
| Characteristics |
genotype: 3' splice site mutation (ag > cc)
treatment: Denatured control 8 mM NMIA
|
| Treatment protocol |
RNAs were treated with 2 mM N-Methylisatoic anhydride (NMIA) for 1 hr at 16 °C or 8 mM NMIA for 30 min at 30 °C or the vehicle (DMSO) under the same conditions
|
| Growth protocol |
Not Applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification by Monarch RNA cleanup kit (New England Biolabs)
cDNA was PCR amplified using primers containing partial Illumina adapter for 20 cycles and then the library was further amplified for 8 cycles with dual index primers
Selective 2′ hydroxyl acylation followed by primer extension by mutational profiling (SHAPE-MaP)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Denatured control 8 mM NMIA
|
| Data processing |
Library strategy: SHAPE-MaP
Basecalls performed with Realtime Analysis (RTA) software launched automatically by MiSeq Control Software
All steps of the processing (including quality control by FastQC, alignment by Bowtie, and mutation counting) were carried out by SHAPEMapper 2.0. Each processed file is generated by counting mutations in DMSO (i.e. untreated), NMIA (i.e. treated), and DC (i.e. denatured control) reads of the corresponding samples.
Supplementary_files_format_and_content: tab-delimited files contain SHAPE reactivity per nucleotide
|
| |
|
| Submission date |
Apr 23, 2021 |
| Last update date |
Jun 23, 2021 |
| Contact name |
Kaushik Saha |
| E-mail(s) |
ksaha79@googlemail.com
|
| Organization name |
University of California San Diego
|
| Department |
Chemistry and Biochemistry
|
| Lab |
NSB 3325A
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093-0375 |
| Country |
USA |
| |
|
| Platform ID |
GPL30034 |
| Series (2) |
| GSE173175 |
Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code [in vitro] |
| GSE173178 |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code |
|
| Relations |
| BioSample |
SAMN18844204 |
| SRA |
SRX10664829 |
