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Sample GSM5261564 Query DataSets for GSM5261564
Status Public on Jun 23, 2021
Title AdML_in_vivo_DMSO
Sample type SRA
 
Source name Transfected into HeLa cells
Organism Human adenovirus 2
Characteristics genotype: wild type
treatment: DMSO 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 DMSO for 15 min at 37 °C
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 SAMN18844469
SRA SRX10664869

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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