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Sample GSM3475303 Query DataSets for GSM3475303
Status Public on Oct 01, 2022
Title DLD1-treatment-2
Sample type SRA
 
Source name colorectal carcinoma
Organism Homo sapiens
Characteristics cell type: epithelial cells
treatment: treatment with RK
Treatment protocol We chose the concentration of 400 μg/mL RK for 72 h to study
Growth protocol DLD-1 cells were cultured in DMEM medium supplemented with 10% Fetal Bovine Serum, 100 U/mL penicillin and 0.1 mg/mL streptomycin at in a 37 °C humidified atmosphere containing 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Total RNA Miniprep Kit (Axygen, Hangzhou, China) according to the supplier’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using TopHat v2.1.0 with default parameters
Transcript assembly and FPKM (RPKM) estimated for RNA-Seq data using Cufflinks v2.2.1.0 with default parameters
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample ...
 
Submission date Nov 15, 2018
Last update date Oct 01, 2022
Contact name Haopeng Zhang
E-mail(s) zhp2008bj@163.com
Phone +86451-82576685
Organization name The Fourth Affiliated Hospital of Harbin Medical University
Department Department of General Surgery & Bio-Bank of General Surgery
Street address No. 37 Yiyuan Street
City Harbin
State/province Heilongjiang
ZIP/Postal code 150001
Country China
 
Platform ID GPL21290
Series (1)
GSE122587 Insights into the mechanism underlying the therapeutic effects of raspberry ketone on human colorectal carcinoma cells revealed by RNA sequencing and bioinformatics analysis
Relations
BioSample SAMN10431977
SRA SRX5012083

Supplementary file Size Download File type/resource
GSM3475303_DLD1-treatment-2.txt.gz 4.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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