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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
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- person_outline Kim-Anh Le Cao
Publication for integrOmics
Exosomes from patients with septic shock convey miRNAs related to inflammation and cell cycle regulation: new signaling pathways in sepsis?
[…] 65-A; Qiagen). Raw data were analyzed using ExpressionSuite v1.0.3 software (Life Technologies/Thermo Fisher Scientific), and all cycle threshold (Ct) values were evaluated using StatMiner version 5 (Integromics, Granada, Spain). Considering the cDNA preamplification step, Ct values greater than or equal to 32 for miRNAs and oxidative stress and greater than or equal to 35 for the immune study wer […]
From Genomics to Omics Landscapes of Parkinson's Disease: Revealing the Molecular Mechanisms
[…] To take into account all the different omics layers, integromics (also termed integratomics or integrated omics) studies aim to find an overlap between results of individual omics. At least four integromics studies done on human samples have been recent […]
Long Noncoding RNA H19 Inhibits Cell Viability, Migration, and Invasion Via Downregulation of IRS 1 in Thyroid Cancer Cells
[…] permix kit (Bio-Rad Laboratories, Hercules, CA, USA). The reaction was performed in triplicate for each sample at least 3 independent runs. The expression levels were analyzed by Real-Time StatMiner (Integromics, Madrid, Spain), and data were calculated by using 2−ΔΔCT method. […]
Alzheimer's brains show inter related changes in RNA and lipid metabolism
[…] pression in RPKM with reference to the RefSeq gene structure; read counts with reference to each gene. Mapping and sequence/quality control metrics were generated both with the Lifetech suite and the Integromics SeqSolve analysis suite on all the samples. Read lengths were 75 nucleotide fragments, with a percentage of genome alignments over the whole sequence length over 80%. The minimal sequence […]
MicroRNA profile in neosquamous esophageal mucosa following ablation of Barrett’s esophagus
[…] a Ct value of 40.To investigate whether any of the samples had low quality data we used the “detector profiling across samples” module in the RealTime PCR Statminer® software analysis program (v4.5, Integromics) to examine the correlations of Ct values between samples from the same epithelial tissue type across all of the amplified microRNAs. Samples that had multiple outliers were excluded from […]
Neuronal expressed microRNA targeted pseudogenes compete with coding genes in the human brain
[…] ion; gene expression in RPKM with reference to the RefSeq gene structure; and read counts with reference to each gene. Quality control metrics were generated both with the Lifetech suite and with the Integromics SeqSolve analysis suite on all the samples. TopHat 2.0.11 and Cufflinks 2.1.1 suite against GRCh38 genome sequence and associated ENSEMBL exon/transcript annotation in gtf format served to […]
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