|
| Status |
Public on Mar 04, 2021 |
| Title |
HEK293_Amoto_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T cells
cell type: embryonic kidney cells
passages: 8-10
|
| Treatment protocol |
0.5 mg/ml AMT or Amotosalen in vivo crosslinking; mRNAs were enriched using Poly(A)Purist™ MAG Kit (Invitrogen); EVD68 viral RNA is enriched using seven antisense oligos.
|
| Growth protocol |
HEK293T and 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 |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
crosslinked total RNA
|
| Data processing |
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 or mm10 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 and mm10
Supplementary_files_format_and_content: bam files contain grouped snRNA structures and interactions; BEDPE file contains disjoint RNA structures and interaction.
|
| |
|
| Submission date |
Apr 28, 2020 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Minjie Zhang |
| E-mail(s) |
minjiezhang123@gmail.com
|
| 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 |
GPL15520 |
| Series (1) |
| GSE149493 |
Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells |
|
| Relations |
| BioSample |
SAMN14752958 |
| SRA |
SRX8188695 |
