NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3913838 Query DataSets for GSM3913838
Status Public on Apr 06, 2020
Title HV-6
Sample type SRA
 
Source name human umbilical vein endothelial cells
Organism Homo sapiens
Characteristics tissue: umbilical cord
genotype: wild type
htnv infection: HTNV infected
Treatment protocol HUVECs were mock-infected or HTNV-infected at a multiplicity of infection (MOI) of 1.
Growth protocol HUVECs were purchased from ScienCell Research Laboratories (Cat No: 8000, Carlsbad, USA) and cultured in ECM Medium with 5% fetal bovine serum (FBS), 1% penicillin-streptomycin and endothelial cell growth supplement (ECGS) (ScienCell) at 37°C in 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA from mock and HTNV-infected HUVECs was isolated with TRIzol reagent (Invitrogen, USA).
rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) , then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. Subsequently, the purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwa mem mapping) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM/SRPBM values and counts for each Sample
 
Submission date Jul 01, 2019
Last update date Apr 06, 2020
Contact name LI LI
E-mail(s) 1805913496@qq.com
Organization name wuhan university school of basic medical sciences
Street address 185 Donghu Road
City Wuhan
State/province Hubei
ZIP/Postal code 430071
Country China
 
Platform ID GPL21290
Series (1)
GSE133634 Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection
Relations
BioSample SAMN12174256
SRA SRX6386411

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap