|
Status |
Public on Jun 23, 2021 |
Title |
AdMLΔ3'SSΔESE_in_vivo_NAI |
Sample type |
SRA |
|
|
Source name |
Transfected into HeLa cells
|
Organism |
Human adenovirus 2 |
Characteristics |
genotype: 3' SS & ESE mutation (cagCT > accTC, TCA > AAT)) treatment: 100 mM NAI for 15 min at 37 degreeC cell line: HeLa
|
Treatment protocol |
Resuspended cells were treated with 2-methylnicotinic acid imidazolide (NAI) for 15 min at 37 °C followed by quenching with 125 mM DTT
|
Growth protocol |
HeLa cells grown in monolayer were transfected with U1 snRNA antisense morpholino oligonucleotide, then with the plasmids expressing the AdML variant under CMV promoter
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted with Trizol 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 |
100 mM NAI for 15 min at 37 °C Ad3E_vv_Ad3E
|
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) |
GSE173177 |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code [In Vivo] |
GSE173178 |
Discovery of pre-mRNA structural scaffold as a contributor to mammalian splicing code |
|
Relations |
BioSample |
SAMN18844457 |
SRA |
SRX10664876 |