|
| Status |
Public on Jul 05, 2022 |
| Title |
AdML_5X SRSF1_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
In vitro transcription
|
| Organism |
Human adenovirus 2 |
| Characteristics |
genotype: wild type
treatment: 5X SRSF1-RE and 3.33% DMSO for 15 min at 30 °C and then 15 min at room temperature
|
| Treatment protocol |
RNAs were treated with 4 mM N-Methylisatoic anhydride (NMIA) for 15 min at 30 °C and 15 in at room temperature or the vehicle (DMSO) under the same conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Proteinase K digestion (where protein is added) 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 Superscrit II and analyzed by SHAPEMapper 2.0 pipeline
Ad-S1_Ad.shape
|
| Data processing |
Library strategy: Selective 2′ hydroxyl acylation followed by primer extension by mutational profiling (SHAPE-MaP)
Basecalls performed with Realtime Analysis (RTA) software launched automatically by MiSeq Control Software
All steps of the processing were carried out by SHAPEMapper 2.0 pipeline
Supplementary_files_format_and_content: .SHAPE
|
| |
|
| Submission date |
Nov 15, 2021 |
| Last update date |
Jul 05, 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) |
| GSE188649 |
[SHAPE-MaP_4_mM] 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 |
SAMN23150927 |
| SRA |
SRX13139011 |
