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Sample GSM2417929 Query DataSets for GSM2417929
Status Public on Jul 28, 2017
Title FN Treatment, 3
Sample type SRA
Source name HT-29 cells
Organism Homo sapiens
Characteristics cell type: human colorectal cancer cells
agent: F. nucleatum
Treatment protocol The cultured F.nucleatum was used to treat the HT29 colorectal cancer cells, while the blank culture medium-teated HT29 CRC cells was used as negative controls.
Growth protocol The human colorectal cancer cells HT-29 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
Extracted molecule total RNA
Extraction protocol total RNA of HT-29 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 Reads were mapped to the human genome (hg19) using TopHat v2.0.11 ( with the following default options with a TopHat transcript index built from Ensembl_GRCh37. Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file.
Genome_build: Ensembl_GRCh37(hg19)
Supplementary_files_format_and_content: count
Submission date Dec 06, 2016
Last update date May 15, 2019
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 (1)
GSE90944 RNA-seq in HT-29 colorectal cancer cells after F. nucleatum treatment
BioSample SAMN06113537
SRA SRX2399055

Supplementary file Size Download File type/resource
GSM2417929_Fn3.count.txt.gz 206.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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