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Sample GSM3386124 Query DataSets for GSM3386124
Status Public on Jul 08, 2019
Title SW480_Control siRNA3
Sample type SRA
 
Source name SW480_Control siRNA
Organism Homo sapiens
Characteristics cell line: SW480
cell type: human colorectal cancer cells
passage: 16-19
genotype/variation: Control siRNA1
Treatment protocol The human lncRNA-AF339830 siRNA were introduced into the SW480 colorectal cells, while nonspecific siRNA was used as negative controls.
Growth protocol The human SW480 colorectal cancer cell 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 SW480 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 2500
 
Description Sample_SW480_AF123_3_20160323_CTTGTA_L007
Data processing Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the 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: hg19
Supplementary_files_format_and_content: count file
 
Submission date Sep 12, 2018
Last update date Jul 10, 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 GPL16791
Series (2)
GSE119866 A novel lncRNA lncRNA-AF339830 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc [RNA-Seq]
GSE132888 A novel lncRNA lncRNA-AF339830 promotes colorectal carcinogenesis and glucose metabolism by stabilizing and specifying the transcription modification pattern of c-Myc
Relations
BioSample SAMN10038543
SRA SRX4673593

Supplementary file Size Download File type/resource
GSM3386124_N3_sort.count.txt.gz 200.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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