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Sample GSM4594773 Query DataSets for GSM4594773
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

Supplementary file Size Download File type/resource
GSM4594773_HEK293_snoRNA_annotation.txt.gz 27.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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