The RNA expression data (level 3) of CRC patients—obtained from 622 CRC cancer tissues and 51 adjacent non-tumor normal tissues (up to June 13, 2018)—were downloaded from the TCGA data portal. The expression profiles of RNA and miRNA from the 673 samples had been derived from the IlluminaHiSeq RNASeq and the IlluminaHiSeq miRNASeq sequencing platforms. The mRNAs, lncRNAs, and pseudogenes were identified based on the annotation from the Ensembl database (http://www.ensembl.org/index.html , version 93). RNAs not included in the Ensembl database were excluded from the present study. We mainly used the R program (R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/ ) for analysis of RNA data. Raw counts data were normalized by the edgeR package [6 (link)] and then transformed by the limma package [7 (link)].
Illuminahiseq mirnaseq
Manufactured by Illumina
Sourced in United States
The IlluminaHiSeq_miRNASeq is a laboratory equipment designed for microRNA sequencing. It uses high-throughput sequencing technology to analyze small RNA molecules, including microRNAs, within a sample.
Automatically generated - may contain errors
14 protocols using illuminahiseq mirnaseq
1
Comprehensive Transcriptomic Analysis of Colorectal Cancer
2
Transcriptomic Profiling of Lung Cancer
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The expression data of lncRNAs, TFs and miRNAs were obtained from LUSC and LUAD tissues and their corresponding adjacent normal tissues as previously described (16 (link)). The raw read counts for each exon were downloaded from The Cancer Genome Atlas (TCGA) (https://portal.gdc.cancer.gov/ ) level 3 dataset, and the human TF and lncRNA annotations from GENCODE were used to map these exons (17 (link)). In order to obtain expression data of human TFs and lncRNAs, the reads per kilobase of transcript per million mapped reads were recalculated for the TFs and lncRNAs. miRNA sequencing data (Illumina HiSeq miRNA Seq; Illumina, Inc., San Diego, CA, USA) of LUAD and LUSC were also downloaded from TCGA (level 3) (7 (link)). Finally, a total of 166 LUAD samples and 9 matched normal samples were selected, whereas 120 LUSC samples and 9 matched normal samples were selected.
3
Profiling of LSCC in TCGA Database
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The Cancer Genome Atlas dataset of laryngeal squamous cell carcinoma. MRNA and miRNA expression profiling of LSCC was downloaded from TCGA (https://tcga-data.nci. nih.gov/tcga/) data portal (12) . A total of 528 patients with head and neck squamous cell carcinoma (HNSC) was available in TCGA and the corresponding clinical records were downloaded. The inclusion criteria were set as follows: (1) The subtype of anatomic organ was the larynx; (2) patients without the history of other malignancy; (3) patients without neoadjuvant treatment. A total of 105 patients with LSCC were included into the study. Level 3 mRNA and miRNA datasets of LSCC patients were generated from UNC IlluminaHiseq_ RNASeqV2 and BCGSC IlluminaHiSeq-miRNASeq, respectively.
4
TCGA TSCC RNA and miRNA Sequencing
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Level 3 RNASeq and miRNASeq data from TSCC samples up to June 30, 2018, including 122 TSCC tissues and 15 normal controls, were downloaded from the TCGA data portal. The sequence data originated from IlluminaHiSeq_RNASeq and IlluminaHiSeq_miRNASeq sequencing platforms; all the data are publicly available.
5
Comprehensive Cancer Genomic Analysis
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TCGA data were downloaded for BRCA (breast), LIHC (liver), LUSC (lung), and PRAD (prostate) cancers from https://portal.gdc.cancer.gov . Tumor samples (TCGA sample type “01”) measured across mRNA IlluminaHiSeq_RNASeqV2 (Level 3), miRNA IlluminaHiSeq_miRNASeq (Level 3), and Affymetrix SNP6.0 platforms were used for the analysis, amounting to 699 total tumor samples in breast, 345 in liver, 341 in lung, and 481 in prostate cancer.
6
Papillary Thyroid Cancer Genomic Profiles
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PTC patients (502) were obtained from the TCGA consortium. Inclusion criteria included: i) patients diagnosed with PTC but with no other malignancies; ii) patients with complete clinical data, including age, sex, race, the American Joint Committee on Cancer (AJCC) TNM and pathologic stage; iii) patients with overall survival time <2,000 days; and iv) patients with complete lncRNA, mRNA and miRNA expression profiles. In total, 348 patients (cohort T) who were pathologically diagnosed as PTC and 58 normal samples (cohort N) were enrolled in downstream analysis. The RNAseq and miRNAseq data (level 3) generated from IlluminaHiseq_RNASeq and IlluminaHiseq_miRNASeq sequencing platform was downloaded from TCGA data portal. The present study followed the publication guidelines of TCGA Research Network (http://cancergenome.nih.gov/publications/publicationguidelines ). Thus, no further ethical approvals were required.
7
Mature miRNA Expression Profiles in LUSC
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The preprocessed LUSC mature miR expression profiles in The Cancer Genome Atlas (TCGA, https://cancergenome.nih.gov/ ) database, displayed as log2 converted reads per million (log2(RPM+1)), were downloaded from University of California Santa Cruz Xena (https://xenabrowser.net/datapages/ , version 09-08-2017). The corresponding clinical information was downloaded from TCGA database (download date 09-26-2018). These contain two mature miR expression data, which are based on two different platforms, including 380 samples (336 LUSC tissues and 44 matched healthy lung tissues) based on the IlluminaHiSeq_miRNASeq platform (Illumina Inc., San Diego, CA, USA) and 131 LUSC tissues based on the IlluminaGA_miRNASeq platform. The samples based on the IlluminaHiSeq_miRNASeq platform were used as the training set to identify differentially expressed miRs and construct a miR-based signature for predicting prognosis, and the samples based on the IlluminaGA_miRNASeq platform were used as the validation set to verify the signature.
8
TCGA HNSCC RNA-seq Data Analysis
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RNA-sequencing data of 546 samples with HNSCC were retrieved from the TCGA data portal1 . The RNA expression data (level 3) and clinical data of 546 HNSCC cases were downloaded from the TCGA data portal. The RNA- and miRNA-sequencing data from the 546 samples which were free to download were derived from the IlluminaHiSeq_RNASeq and IlluminaHiSeq_miRNASeq sequencing platforms. The sequencing data of the 546 samples contained the corresponding RNA-seq and miRNA-seq data and were divided into 502 tumor samples and 44 normal samples. In the current study, we mainly took the program code written in Perl and R language to analyze RNA data.
9
Identifying Prognostic miRNA Signatures in ccRCC
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The preprocessed ccRCC mature miRNA expression profiles in TCGA database, displayed as log2 converted reads per million (log2 (RPM + 1)), and clinical information, were downloaded from the UCSC Xena (https://xenabrowser.net/datapages/ , version 09-08-2017). It contains miRNA expression data from two different platforms, including 311 samples (241 ccRCC tissues and 70 matched normal kidney tissues) based on the IlluminaHiSeq_miRNASeq platform (Illumina Inc., San Diego, CA, USA) and 259 ccRCC tissues based on the IlluminaGA_miRNASeq platform. The samples based on the IlluminaHiSeq_miRNASeq platform were used as the training set to identify differentially expressed miRNAs and to construct a miRNA-based signature for predicting prognosis. The samples based on IlluminaGA_miRNASeq platform were used as the test set to verify the signature. The mature miRNA sequencing data were processed using R language.
10
PTEN Expression Profiling in Breast Cancer
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Data on RNA expressions and clinical features of BC samples and adjacent tissues were downloaded from TCGA database (https://portal.gdc.cancer.gov/ , accessed on 21 December 2021), and RNA and miRNA sequences were obtained from IlluminaHiSeq_RNASeq and IlluminaHiSeq_miRNASeq sequencing platforms. All data could be freely downloaded. In terms of the median PTEN expression, 1059 BC samples were divided into PTENhigh group (n = 529) and PTENlow group (n = 530). Against the requirements of data integrity, the samples with missing items were excluded. Finally, data of 1000 patients were obtained from BC samples, and the caret package was further randomly allocated to the training set and the test set at a ratio of 7: 3. In addition, the GSE21422 data set was downloaded from GEO database (https://www.ncbi.nlm.nih.gov/gds/ , accessed on 17 July 2022) to verify the expression of RNAs in the model.
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