NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3760165 Query DataSets for GSM3760165
Status Public on May 09, 2020
Title Con
Sample type SRA
 
Source name Abelson murine leukemia virus-induced tumor
Organism Mus musculus
Characteristics tissue: ascites
cell line: RAW 264.7
passages: 10-15
treatment: control
Treatment protocol RAW 264.7 cells were treated with 0.5mM hydroxyurea (HU, H8627, Sigma Aldrich) and gold nanoparticles at same time, then cultured for 12 hours.
Growth protocol The murine-derived macrophage cell line RAW 264.7 cells (China Center for Type Culture Collection, CCTCC) was used. RAW 264.7 cells cultured in Dulbecco’s modified Eagle Medium (DMEM) containing 10% fetal bovine serum (FBS, Gibco, Life Technologies Corporation) and 1% penicillin/streptomycin (P/S, HyClone, Thermo Fisher Scientific Inc). All cultures were performed at 37℃ in a humidified 5% CO2 atmosphere.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNAiso Plus (TaKaRa Bio Inc., Japan) following the manufacturer’s protocol.
Library preparations were constructed according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina®)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Base-calling using Bcl2fastq (v2.17.1.14)
Filtering using Cutadapt(version 1.9.1)
Clean data were aligned to the mm10 genome via software Hisat2(v2.0.1)
Estimate gene and isoform expression levels from the pair-end clean data using HTSeq (v0.6.1)
Differential expression analysis used the DESeq Bioconductor package,P value <0.05
GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05;use scripts in house to enrich significant differential expression gene in KEGG pathways.
Novel transcripts can be predicted via results of Cuffcompare
Alternative splicing analysis using Asprofile v1.0
Samtools v0.1.18 with command mpileup and Bcftools v0.1.19 were used to do SNV calling
Usage of exons caused by the experimental condition(DEU) was analysed by Bioconductor package DEXSeq (V 1.21.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample
 
Submission date May 10, 2019
Last update date May 09, 2020
Contact name Miusi Shi
E-mail(s) sms@whu.edu.cn
Phone 18907137537
Organization name The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei MOST)
Department School of Stomatology
Lab Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology
Street address No.237 in Luoyu Road
City Wuhan
State/province Hubei
ZIP/Postal code 430079
Country China
 
Platform ID GPL21273
Series (1)
GSE131033 Nano gold simulated autophagy prevents cell death
Relations
BioSample SAMN11619096
SRA SRX5818212

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