|
| Status |
Public on Jul 05, 2022 |
| Title |
RNP_AdML + SRSF1 + SDA |
| Sample type |
SRA |
| |
|
| Source name |
In vitro transcribed from a plasmid
|
| Organism |
Human adenovirus 2 |
| Characteristics |
genotype: wild type
treatment: SRSF1 and 4 mM SDA at 4 °C for 2 hours with rocking
|
| Treatment protocol |
RNAs were treated with 4 mM SDA (NHS-diazirine, succinimidyl 4,4′-azipentanoate) for 2 hours at 4 °C with rocking or the vehicle (DMSO) under the same conditions followed by exposure to 3 J/cm2 of 365 nm UV light
|
| Growth protocol |
Not Applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Proteinase K digestion followed by 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
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Reverse transcribed with Superscript II and analyzed by SHAPEMapper 2.0 pipeline
|
| Data processing |
library strategy: RNA-protein interactions by mutational profiling (RNP-MaP)
Basecalls performed with Realtime Analysis (RTA) software launched automatically by MiSeq Control Software
Per-nucleotide mutation frequencies (number of mutation events/effective read depth) for both crosslinked (SDA + UV-treated) and uncrosslinked (UV-treated) samples were calculated from output ShapeMapper 2 profiles.
RNP-MaP ‘Reactivity’ was computed as the ratio of nucleotide crosslinked mutation frequency to un-crosslinked mutation frequency (SDA + UV rate/UV-only rate).
To be designated as RNP-MaP sites, nucleotide positions had to pass three quality filters: 1) sites were required to have at least 50 more mutation events in the SDA + UV-treated sample than the UV-treated sample; 2) site reactivities had to exceed the nucleotide-dependent empirical thresholds described in the next section; and 3) nucleotide reactivities were required to achieve a Z′ factor greater than 0.
Details can be found in Weidmann CA et al. (2021). Nat Biotechnol, 39, 347-356
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: NOT PROVIDED
|
| |
|
| Submission date |
Nov 11, 2021 |
| Last update date |
Jul 06, 2022 |
| 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) |
| GSE188650 |
[RNP-MaP] U1 snRNP regulates recruitment of early spliceosomal components by disrupting SRSF1-pre-mRNA interactions |
| GSE188652 |
Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly |
|
| Relations |
| BioSample |
SAMN23075160 |
| SRA |
SRX13114867 |
