|
Status |
Public on Mar 04, 2021 |
Title |
HEK293_snoRNA |
Sample type |
SRA |
|
|
Source name |
HEK293T cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 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 |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
crosslinked snoRNA
|
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 |
Jun 08, 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 |
GPL24676 |
Series (1) |
GSE149493 |
Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells |
|
Relations |
BioSample |
SAMN15166413 |
SRA |
SRX8496030 |