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Sample GSM7124400 Query DataSets for GSM7124400
Status Public on Aug 09, 2023
Title Ls174 cells, Control 3
Sample type SRA
Source name Ls174
Organism Homo sapiens
Characteristics cell line: Ls174
cell type: Colon cancer cells
genotype: WT
treatment: no treatment
time: 24 hrs
Treatment protocol 3x10^5 treated Ls174 and HepG2 cells were cultured with 0.7 mg/ml extract from Hypnea musciformis for 24 hr
Growth protocol Ls174 and HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol (MRC). 1 ug of total RNA was used for the construction of sequencing libraries.
3’ RNA libraries for RNA-seq were prepared using the 3’mRNA Quant Library Prep kit protocol of Ion Torrent following manufacturer's protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
Data processing HISAT2-BOWTIE2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic
Trimmed sequence reads were mapped to GRCh37/hg19 using hisat2 (parameters -un, --add-chrname). Hisat2 unaligned reads were mapped with BOWTIE2 (parameters --local –very-sensitive-local). Hisat2 and Bowtie2 aligned reads were merged.
Read count extraction and normalization were performed using the metaseqR2 Bioconductor package
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Submission date Mar 30, 2023
Last update date Aug 09, 2023
Contact name Antonis Giakountis
Organization name University of Thessaly
Department Biochemistry and Biotechnology
Street address Biopolis-Mezourlo
City Larissa
ZIP/Postal code 41500
Country Greece
Platform ID GPL17303
Series (1)
GSE228578 Transcriptomics and proteomics analyses reveal the anti-cancer properties of extract from Hypnea musciformis macroalgea in liver and intestinal cancer cells
BioSample SAMN33988203
SRA SRX19821217

Supplementary file Size Download File type/resource
GSM7124400_Ls174_CON_3.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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