|
| Status |
Public on Jan 14, 2020 |
| Title |
U4_6_core_domain |
| Sample type |
SRA |
| |
|
| Source name |
U4_6_core_domain
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: NA
sample type: In vitro transcribed RNA
molecule subtype: DMS-modified RNA
|
| Treatment protocol |
DMS-treatment for RNA secondary structure analysis, between 0.2-2% DMS at 37C for 5 minutes
|
| Growth protocol |
In vitro transcribed and DMS modified RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
DMS-treated cells were pelleted and resuspended in 1 mL Trizol, RNA was extracted by chloroform extraction and isopropanol precipitation.
3'Phosphorylation with rSAP, linker ligation with T4 RNA ligase truncated KQ, excess linker degraded with RecJ and 5'Deadenylase. rRNA was subtracted with RiboZero, and RT was performed with TGIRT-III. cDNAs were isolated by gelextraction on a 10% TBE-Urea gel and extracted by isopropanol precipitation. cDNAs were circularized with circLigase and amplified by PCR with phusion polymerase. PCR products were purified by gel extraction from an 8% TBE gel and isopropanol precipitation. Samples were quantified by Bioanalyzer.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Library strategy: DMS-MaPseq
Alignment with bowtie2 (2.3.4.1)
Read trimming (TrimGalore v0.4.1) and QC (FastQCv0.11.8)
DREEM Clustering (custom code available at https://gitlab.com/Corbin-Rouskin/RNA_structure/tree/gpu)
RNAstructure(v6.0.1) folding and VARNA (v3.93) visualization
Genome_build: Adenosine deaminase (add) riboswitch corresponds to nucleotides 1590535-1590663 of V.vulnificus strain (Genbank Accession code CP037932.1). The U4/6 core-domain RNA construct is based on the interface of the U4 and U6 snRNA (Genbank accession code 2N7M_X).
Supplementary_files_format_and_content: _Mu.txt files produced by DREEM clustering algorithm
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Jan 14, 2020 |
| Contact name |
Silvi Rouskin |
| Organization name |
Whitehead Institute
|
| Street address |
455 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE131506 |
HIV-1 RNA structure and heterogeneity analysis |
|
| Relations |
| BioSample |
SAMN13762638 |
| SRA |
SRX7521432 |
