TFROBMZTJT1PSUBM
RNA-seq Analysis PortalUSER MANUAL
Manual forQIAGEN RNA-seq Analysis Portal 1.1.1August 10, 2021This software is for research purposes only.QIAGEN AarhusSilkeborgvej 2PrismetDK-8000 Aarhus CDenmarkQIAGEN RNA-seq Analysis Portal 1.1.1 User Manual2
ContentsIntroduction6General information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6Intended use statement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6General Description7Deployment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7Supported sample kits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7Accessing RNA-seq Analysis Portal . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8Analysis credits for RNA-seq Analysis Portal . . . . . . . . . . . . . . . . . . . . . . . .9Getting Started11Upload sequencing data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11Align and count . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .13Create experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .16Filter features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18Save results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19Next steps in GeneGlobe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19User Interface22RNA-seq Analysis Portal terminology and data organization . . . . . . . . . . . . . . . .23Analysis Portal page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .24QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual3
Samples page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Starting Analysis2628Align and count dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .28Create experiment dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .29Compare analyses dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .33Viewing Results34Samples and Quality Control report. . . . . . . . . . . . . . . . . . . . . . . . . . . .34Differential expression view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .36Comparison view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .42RNA-seq Analysis Portal analysis explained43Align and count analysis workflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . .43Create experiment analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . .46Compare analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .47Appendix A - Sequence file naming pattern48Appendix B - Reference and annotation information50General references and annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . .50Sample kit specific resources51. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Appendix C - Analysis workflow parameters52QIAseq miRNA Library Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .53QIAseq UPX 3' Transcriptome Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .55QIAseq Stranded mRNA Select/Stranded Total RNA Lib Kit . . . . . . . . . . . . . . . .58TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin) . . . . . . . . . . .60Illumina Stranded Total RNA Prep with Ribo-Zero Plus . . . . . . . . . . . . . . . . . . .62NEBNext Ultra II Directional RNA Library Prep Kit for Illumina . . . . . . . . . . . . . . .64QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual4
KAPA RNA HyperPrep Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .66SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian/Low Input Mammalian .68Collibri Stranded RNA Library Prep Kit for Illumina Systems . . . . . . . . . . . . . . . .70Appendix D - Latest improvements for QIAGEN RNA-seq Analysis Portal72RNA-seq Analysis Portal 1.1.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72RNA-seq Analysis Portal 1.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .73RNA Analysis Portal 1.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .75QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual5
IntroductionThis manual is for QIAGEN RNA-seq Analysis Portal 1.1.1.General informationTechnical assistanceIf you have questions about or difficulties using QIAGEN RNA-seq Analysis Portal, please contactus by filling in the web-based contact form at l-support/technical-support-form/.We also appreciate your feedback to help us improve our products and documentation.Policy statementIt is QIAGEN's policy to improve products as new techniques and components become available.QIAGEN reserves the right to change the specifications of products at any time.How to cite RNA-seq Analysis PortalPlease use the following when citing this product:QIAGEN RNA-seq Analysis Portal 1.1.1 (QIAGEN, Aarhus, Denmark),https://rnaportal.qiagen.comIntended use statementQIAGEN RNA-seq Analysis Portal is for research use only.QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual6
General DescriptionRNA-seq Analysis Portal is a cloud-based platform for analyzing your RNA-seq expression data,accessible from a web browser. In just a few steps, the predefined analysis pipelines letyou calculate expression levels, identify differential expression, as well as identify significantpathways, regulators, diseases and functions.The graphical views and interactive plots enable seamless exploration and refinement of resultsbefore you pass them to QIAGEN GeneGlobe Design and Analysis Hub for exploration and planningof next steps, for example qPCR or dPCR-based follow up experiments for your filtered targetgenes.RNA-seq Analysis Portal is powered by QIAGEN CLC Genomics and QIAGEN Ingenuity PathwayAnalysis.The underlying software used for secondary analyses is CLC Genomics Server 21.0.3 andBiomedical Genomics Analysis plugin 21.0.1.DeploymentRNA-seq Analysis Portal is deployed on Amazon Web Services, US East (Northern Virginia) Region.Supported sample kitsRNA-seq Analysis Portal supports analysis of FASTQ data generated on Illumina instrumentsusing the following sample kits:QIAGEN QIAseq Stranded mRNA Select Kit QIAseq Stranded Total RNA Lib Kit QIAseq miRNA Library Kit QIAseq UPX 3' Transcriptome KitQIAGEN RNA-seq Analysis Portal 1.1.1 User Manual7
Illumina TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin) Illumina Stranded Total RNA Prep with Ribo-Zero PlusNew England Biolabs NEBNext UltraTM II Directional RNA Library Prep Kit for IlluminaRoche Sequencing solutions KAPA RNA HyperPrep KitTakara Bio SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian SMARTer Stranded Total RNA Sample Prep Kit - Low Input MammalianThermo Fisher Scientific CollibriTM Stranded RNA Library Prep Kit for Illumina SystemsData is analyzed using dedicated analysis workflows. Details specific to a given analysis workfloware provided in later sections. The main steps in an expression analysis are: Reads are aligned and counted to produce expression values for the individual samples(Align and count). Expression levels between groups of samples are compared in an experiment, producingone or more differential expression outputs (Create experiment).Accessing RNA-seq Analysis PortalRNA-seq Analysis Portal is accessed using a web browser, either via the QIAGEN GeneGlobeDesign and Analysis Hub or directly: QIAGEN GeneGlobe Data Analysis Center: https://geneglobe.qiagen.com/analyze.How to log in is described below.QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual8
Direct link: https://rnaportal.qiagen.com. Use your My QIAGEN account creden-tials to log in.Logging in from the QIAGEN GeneGlobe Data Analysis CenterTo log into RNA-seq Analysis Portal from GeneGlobe Data Analysis Center (figure 1):1. Select one of the supported sample kits, or click the button Non-QIAGEN Kits and selectthe third-party kit provider.2. Click Start your analysis. This opens RNA-seq Analysis Portal in a new browser tab.Figure 1: Accessing RNA-seq Analysis Portal from the QIAGEN GeneGlobe Data Analysis CenterSupported browsersRNA-seq Analysis Portal is supported on recent versions of Chrome , Firefox , and Safari . TheRNA-seq Analysis Portal interface is optimized for a minimum screen width of 1024 pixels.Analysis credits for RNA-seq Analysis PortalTo run the initial Align and count analysis in RNA-seq Analysis Portal you will need analysis credits.You can add analysis credits to your account using either the lot number of your QIAseq RNAsample kit or an analysis credit code following the steps below. If you will be using a QIAseq RNAsample kit lot number, you can skip the step Purchase analysis credits.1. Purchase analysis credits. You can purchase analysis credits on its. Choose between GeneGlobe Analyze RNAQIAGEN RNA-seq Analysis Portal 1.1.1 User Manual9
seq (12), or GeneGlobe Analyze RNA-seq (24). Once you have placed your order, you willreceive an email with the analysis credit code.2. Redeem analysis credits. You can redeem analysis credits using a lot number fromone of the supported QIAseq RNA sample kits or an analysis credit code at its/redeem-credits. Forinstructions on how to locate the lot number, see figure 2.Figure 2: The lot number is on the label of your RNA sample kit box.Your analysis credit balance and credit history is provided on the QIAGEN GeneGlobe DataAnalysis Center dashboard.Your analysis credit balance is also shown at the top, right side of the Analysis Portal page,described in the chapter Getting Started.QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual10
Getting StartedRNA-seq Analysis Portal guides you through your RNA expression analysis in 5 steps, indicated bynumbered circles in the user interface:1. Upload sequencing data2. Align and count3. Create experiment4. Filter features5. Save resultsWhen you log into RNA-seq Analysis Portal, you will find steps 1-3 at the top of the Analysis Portalpage (figure 3).Your analysis credits, including the number reserved for running analyses, are displayed in thetop right corner, just under your name.Figure 3: Analysis steps 1 to 3 are accessed from the top of the Analysis Portal page. This is also where you find your analysiscredit balance.Upload sequencing dataBefore you can start an analysis, the FASTQ files must be available to RNA-seq Analysis Portal.This section describes how to upload data from your local system. If your sequencing data isstored in Illumina BaseSpace, you can go straight to the Align and count step.QIAGEN RNA-seq Analysis Portal 1.1.1 User Manual11
To upload data from your local system:1. Click on the Upload data button at the top of the Analysis Portal page. This opens a newbrowser tab with the RNA-seq Analysis Portal sequencing data uploader.2. Select up to 50 FASTQ files at a time in the box on the left side, either by drag-and-droppingor by clicking on browse to select them.3. In the File to sample section on the right, check that the selected FASTQ files group intosamples as expected (figure 4). Grouping is based on FASTQ file naming. If the samplegrouping is not as expected, please check and adjust the file names as necessary. SeeAppendix A for information about the expected naming pattern.4. Click on Upload files.Do not refresh or close the tab until the upload has completed.When your data upload is complete, go back to the RNA-seq Analysis Portal tab.Uploaded FASTQ data is kept for 72 hours. To avoid having to upload the data once again, startthe align and count analysis within this time frame.Note: If you upload FASTQ files for the sam
TruSeq Stranded Total RNA Library Prep (Human/Rat, Gold, Globin) Illumina Stranded Total RNA Prep with Ribo-Zero Plus New England Biolabs NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina Roche Sequencing solutions KAPA RNA HyperPrep Kit Takara Bio SMARTer S
coronavirus and are considered ‘extremely vulnerable’. They include: people with severe respiratory conditions including all cystic fibrosis, severe asthma and severe COPD people on immunosuppression therapies sufficent to significantly increase risk of infection people with specific cancers or receiving cancer treatment. There are more groups in this list, so please visit the .
Anatomy of a journal 1. Introduction This short activity will walk you through the different elements which form a Journal. Learning outcomes By the end of the activity you will be able to: Understand what an academic journal is Identify a journal article inside a journal Understand what a peer reviewed journal is 2. What is a journal? Firstly, let's look at a description of a .
Interpretations ASME A17.1 Safety Code for Elevators and Escalators Appendix B Background - ASME A17.1, an American National Standard First edition published January 1921 Sponsored by American Engineering Standards Committee AESC January 1922 Several iterations later, ANSI became incorporated in October 1969 17th edition of the Code issued April 30, 2004 and effective October .
Nombor / salinan hakmilik terlibat. Bahagian Penilaian 2007 Jabatan Tanah dan UKur, Sabah . pelan pengambilan tanah dan surat . Hasil Bumi untuk disemak oleh Jabatan Peguam Besar Negeri Sesudah disemak dan jika dikembalikan ke JTU untuk pembetulan [jika ada pindaan], deraf pemberitahuan pewartaan baru (digital dan salinan .
This policy covers the implementation of the Corporate Purchasing Card Program and establishes minimum standards for possession and use of corporate purchasing cards. The Corporate Purchasing Card Program was established to save the state time and money. By allowing the bank and the merchants to process most of the paperwork,
Crafting and Executing Strategy, 22e (Thompson) Chapter 1 What Is Strategy and Why Is It Important? 1) Managerial considerations in determining how to compete successfully do not normally include A) How can a company attract, keep, and please customers? B) How can a company modify its entire product line to emphasize its internal service .
Although trading began with floor trading of traditional agricultural commodities such as grains and livestock, exchange-traded futures have expanded to include metals, energy, currencies, equity indexes and interest rate products, all of which are also traded electronically. FUTURES Standardized contracts for the purchase
100 Mansell Ct, E, Ste 500 Roswell, GA 30076 800-306-1330 www.merritthawkins.com Overview 2 Key Findings 4 Recruiting Engagement Characteristics and Metrics 6 Trends and Observations 16 Conclusion 46 1994 - 2020 27 TH EDITION An Overview of the Salaries, Bonuses, and Other Incentives Customarily
