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| Status |
Public on Jun 12, 2017 |
| Title |
siControl 4H Hypoxia |
| Sample type |
SRA |
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| Source name |
Colorectal
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
transfection: siControl
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| 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 ...
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| Submission date |
Nov 28, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Matteo Pallocca |
| Organization name |
Italian National Cancer Institute "Regina Elena"
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| Street address |
Via Fermo Ognibene
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| City |
Rome |
| ZIP/Postal code |
00144 |
| Country |
Italy |
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| Platform ID |
GPL10999 |
| Series (1) |
| GSE90599 |
Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization |
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| Relations |
| BioSample |
SAMN06114046 |
| SRA |
SRX2400116 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2407512_siControl_4H.bigWig |
201.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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