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Sample GSM4888910 Query DataSets for GSM4888910
Status Public on Nov 08, 2023
Title Exosomes derived from HCT116 Cell line untreated-replicate 2
Sample type SRA
 
Source name Exosomes derived from HCT116 cells
Organism Homo sapiens
Characteristics cell line: HCT116
cell type: human colorectal cancer cells
passage: 16-19
Treatment protocol HCT116 Cells were co-cultured with ETBF for 6h. Multiplicity of infection (MOI) was 500. The normal control samples were treated with the bacteria medium without ETBF.
Growth protocol HCT116 cells were routinely cultured adherently in the petri dish with 1640 medium
Extracted molecule total RNA
Extraction protocol Exosomes from conditioned media were collected through standard centrifugation steps, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100 ng of total RNA for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 3000
 
Data processing single-end reads were filtered and trimmed using software Trimmomatic
Quality control before and after raw reads preprocessing was done using software FastQC
Count files of the aligned sequencing reads were generated by the featurecount, using the GFF annotation file from miRBase-v20
Genome_build: GRCh37.p5
Supplementary_files_format_and_content: Tab-separated matrices with read counts,
 
Submission date Nov 08, 2020
Last update date Nov 08, 2023
Contact name Haoyan Chen
Organization name Renji Hospital
Street address 145 Shandong Road
City Shanghai
State/province Shanghai
ZIP/Postal code 200001
Country China
 
Platform ID GPL21290
Series (2)
GSE161048 The Enterotoxigenic Bacteroides fragilis (ETBF) in intestinal inflammation and colorectal carcinogenesis [exosomes]
GSE161049 The Enterotoxigenic Bacteroides fragilis (ETBF) in intestinal inflammation and colorectal carcinogenesis
Relations
BioSample SAMN16705009
SRA SRX9457006

Supplementary file Size Download File type/resource
GSM4888910_ETBF_exo_2.count.txt.gz 8.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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