|
| Status |
Public on Dec 08, 2021 |
| Title |
HeLa_5mM_RNaseR0h |
| Sample type |
SRA |
| |
|
| Source name |
HeLa cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: epithelial cells
crosslinker: 5mM SHARC
passages/age: 8-10
molecule subtype: crosslinked total RNA
|
| Treatment protocol |
5mM, 12.5mM and 25mM SHARC in vivo crosslinking; RNaseR (E049, ABM) were used to trim 3'end of RNA fragments.
|
| Growth protocol |
HeLa cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) + 10% fetal bovine serum (FBS, Gibco) + Pen/Strep antibiotic, in 37°C incubator with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TNA method was used to extract crosslinked RNA.
Library was prepared using optimized PARIS protocol (Lu. et al. Cell, 2016).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: SHARC-seq
Sequencing data were preprocessed to remove adapters form the 5'end and 3’end using Trimmomatic software; PCR duplicates are removed using splitFastqLibrary (in the icSHAPE pipeline)
Reads were mapped to hg38 genome using STAR program.
The primary mapping alignments were filtered to remove low-confidence segments, rearranged and classified into six different types using gaptypes.py (https://github.com/zhipenglu/CRSSANT).
Filtering alignments were assembled to DGs and NGs using the crssant.py script (https://github.com/zhipenglu/CRSSANT).
Bedtools v2.25.0 was used to annotate gapped and chimeric alignments.
Genome_build: hg38
Supplementary_files_format_and_content: BEDPE file contains disjoint RNA structures and interaction.
|
| |
|
| Submission date |
Feb 26, 2021 |
| Last update date |
Dec 09, 2021 |
| Contact name |
Minjie Zhang |
| E-mail(s) |
[email protected]
|
| Phone |
+1-6467314151
|
| Organization name |
University of Southern California
|
| Department |
Department of Pharmacology and Pharmaceutical Sciences
|
| Lab |
Zhipeng Lu
|
| Street address |
1985 Zonal Avenue
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE167812 |
SHARC-seq: High throughput in vivo determination of 3D RNA structures and dynamics |
|
| Relations |
| BioSample |
SAMN18077043 |
| SRA |
SRX10181454 |
