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Sample GSM2407511 Query DataSets for GSM2407511
Status Public on Jun 12, 2017
Title SiChe-1
Sample type SRA
 
Source name Colorectal
Organism Homo sapiens
Characteristics cell line: HCT116
transfection: SiChe-1
Extracted molecule total RNA
Extraction protocol HCT116 cell line was transfected with siChe-1 or siRNA negative control using Lipofectamine 3000 (Life Technologies), total RNA was extracted from cells using TRIzol reagent (Life Technologies) in accordance with the manufacturer's instructions.
Quantity and integrity of the extracted RNA were assessed by NanoDrop Spectrophotometer (NanoDrop Technologies) and by Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. RNA libraries for sequencing were generated according to the standard Illumina TruSeq RNA sample preparation protocol using 2ug total RNA as starting material. The resulting library was controlled qualitatively with the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA) and quantitatively with real-time analysis employing a SYBR Green qPCR protocol with specific primers complementary to adapter sequences. Therefore, only the adapter-ligated fragments that are appropriate for sequencing were quantified. Based on the qPCR quantification, libraries were normalized to 1 nM and denatured by using 0.1N NaOH. Cluster amplification of denatured templates was carried out according to manufacturer protocol (Illumina, Inc., San Diego, CA, USA). Sequencing was performed on a Genome Analyzer IIx (Illumina) in paired-end mode, sequencing from each side 51 bp.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Data processing Raw data was analyzed via RAP pipeline at CINECA, that comprises of read mapping via Tophat and transcript-gene expression abundance estimation via Cufflinks. Differential expression was calculated via Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Nov 28, 2016
Last update date May 15, 2019
Contact name Matteo Pallocca
Organization name Italian National Cancer Institute "Regina Elena"
Street address Via Fermo Ognibene
City Rome
ZIP/Postal code 00144
Country Italy
 
Platform ID GPL10999
Series (1)
GSE90599 Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization
Relations
BioSample SAMN06114047
SRA SRX2400115

Supplementary file Size Download File type/resource
GSM2407511_siChe.bigWig 202.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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