|
| 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 |
