Animal Expression Database USER`S MANUAL
Contents
1. s Manual 3 0 Getting Started 2 0 GETTING STARTED 2 1 Logging On Registering Depending on whether the system is being used for the first time you may need to register by clicking Register at the top right part on the landing page at www anexdb org ANEXdb Register Mozilla Firefox File Edit View History Bookmarks Tools lt A e a E httpsffwww anexdb orgiregister php b IG 4 gt Getting Started E Latest Headlines svn ANEXdb Animal Expr 1 ANEXdb Animal Expression _ ANEXdb Animal Expression LJ ANEXdb Animal Expression L ANEXdb Animal Expression LJ ANEXdb Animal Expression ANEXdb Register G ANEXO ANEXdb Animal Expression Database Home Search Help Register Login ANEXdb gt Register Register Email address Re enter email address First name Last name Job title Head of lab Lab name Institution Street address City State Country SelectaCounty Zip Code 2 start fa anexdb org default 3 anexdb org default Jaya anxdbojsrcjed user manual Micros ANEXdb Register Filling in all the fields besides mandatory is recommended so that the admin can track the submissions When you register it is only required that you enter an email address and password but the more of the other details you enter here the less you will have to enter later when subm2. 00 00 00 testing_new_jar Mus musculus Sushain Pandit 2009 01 02 00 00 00 Gene expression profiles of fasting induced changes in liver and fat tissues of pigs expressing the MC4R D298N variant Sus scrofa Sender Lkhagvadorj 2008 09 19 00 00 00 Another Test by Neeraj Horno sapiens koul 2008 08 27 00 00 00 A test Experiment Remove Homo sapiens neeraj koul 2008 08 26 00 00 00 Expression data from non infected and Salmonella Choleraesuis infected mesenteric lymph nodes Sus scrofa Keith Callenberg 2008 06 30 00 00 00 Analysis of differential gene expression in Salmonella shedder vs non shedder pigs Sus scrofa Jolita Uthe 2008 04 02 00 00 00 Expression data from non infected and Salmonella Typhimurium infected mesenteric lymph nodes Sus scrofa remy younes 2008 03 28 00 00 00 Done tg stan fa anexdb org default 9 anexdb org default Java C user manual Micros User s Manual Page 5 1 5 0 Important Instructions and FAQs 5 2 Regarding soft files and zip archives Upon clicking on the experiment in Search Results you will be presented by the experiment page with download links for soft and a zip archive The soft file is accordance with GEO guidelines This file refers other experiment related files like chp and cel Incase of any missing valules that the system couldn t find there would be a placeholder anexdb_admin insert value here This field would indicate that there has been some missing information in
3. 3 2 3 0 Using the System 3 3 Hybridizations page ANEXdb Submit Hybridizations Microsoft Internet Explorer File Edit View Favorites Tools Help a Q E a Pp search Favorites gt od 2 Address http www anexdb org submit hybrids php Google G ir Bookmarksy Bhoblocked P Check vw Autotnk SE AutoFill a Send tow settingsw Q 7 Web Search S Bookmarks Misettings Mail gt Yahoo Edanswers Games 5 News i shopping ANEXdb Submit Hybridizations Add Tab A Hybridization ANEXdb follows the guildlines for a GEO SOFT submission For a full description go here Select Array Design Choose an Array Design M GEO Accession Number GSM Select CEL File Choose a CEL File v Select CHP File Choose a CHP File v Factors Sample Select Organism Select an Organism v Organism Part Pati Sample Molecule total RNA v Labeling Compound Sample Description T Treatment Prataral 1 Y amp gt El Done Internet a 77 start anexdb org default 8 anexdb org default Java anxdbo src ed user manual Micros ANEXdb Help Mozill A ANEXdb Submit Hy Following is a general guideline for entering the data on this page Array Design This drop down menu lists all of the Affymetrix chips currently loaded If your experiment used a chip th
4. submission if required seen 5 3 User s Manual 1 0 General Information 1 0 GENERAL INFORMATION User s Manual 1 0 General Information 1 0 GENERAL INFORMATION 1 1 System Overview ANEXdb allows scientists to store and analyze gene expression data in the form of microarray experiments Currently Affymetrix is the only platform supported The ANEXdb database schema is available here The underlying functions performed by the system are storage and query based retrieval The system is broadly based on a web based 3 tier architecture User access mode is essentially restricted via the web based client System status is Operational 1 2 References This document was prepared as is by the ANEXdb core development team Refer www anexdb org 1 3 Authorized Use Permission This system is protected from unauthorized usage and or making unauthorized copies of data software pieces etc For further information on this please get in touch with the point of contact s Refer 1 4 1 4 Points of Contact Please drop a note to simius Oiastate edu for queries or feedback 1 5 Acronyms and Abbreviations ANEXdb Animal Expression Database NSF National Science Foundation USDA United States Department of Agriculture User s Manual Page 1 1 1 0 General Information User s Manual Page 1 2 3 0 Getting Started 2 0 GETTING STARTED User
5. the factors and methods used in the experiment here Visibility Here you will set whether you would like the experiment to be available to the public Public visibility is the default setting and allows anyone to view your experiment and data Private keeps the experiment hidden so that only you can view it If you are a member of a Group you will also be able to choose group visibility and that group so that only you and other members of your group can view the experiment User s Manual Page 3 1 3 0 Using the System GEO accession number optional If your experiment has already been submitted and reviewed by NCBI GEO you can enter the GDS or GSE accession number here Experiment Design Enter the Factors and Levels of your experiment here For example if your experiment is a time course experiment with four time steps you would enter Time in the Factor box and 4 in the Number of Levels box If you have only this factor you would then click Refresh Factors to enable 4 text boxes so that you could enter your levels e g 4 hours 8 hours 16 hours 24 hours Publications optional If a journal article related to this experiment has already been published you can enter the article details here Links optional If you have a website with supplementary material about this experiment you can enter that link here 3 2 Uploading associated files ANEXdb Submit Upload Microsoft Internet Explorer TER File Edit V
6. Animal Expression Database User s MANUAL ao 22h UNIVERSITY Revision Sheet Revision Sheet Release No Date Author Revision Description User s Manual First cut Added Section 3 Added Sections 4 amp 5 po pem User s Manual Pag 1 0 2 0 3 0 4 0 5 0 1 0 General Information USER S MANUAL TABLE OF CONTENTS Page GENERAL INFORMATION 22 22 ada 1 1 1 1 System Guau e pb 1 1 1 27 References israelita 1 1 1 3 Authorized Use Permission uu sasana tds 1 1 1 4 Pointsel Contagtiu usus al ef iria aia ieh 1 1 1 5 Acronyms and Abbreviations ipee tese e eee upas un atus ste 1 1 GETTING STARTED en tfe iet mme ee oed 2 1 ZA Logging Once teer e dias 2 1 2 2 Dashboard tree tati eee te e A 2 2 2 3 Exiting the System aie een Li e blew estes iii ce oreet dc edo uoce 2 3 USING THE SYSTEM 2 erede a 3 1 31 Submitting an experiment ient e ls pila 3 1 3 2 Uploading associated files een a eo 3 2 3 3 Hybridizations pasei arena aan Benni 3 3 3 4 Review Page B H 3 4 QUERYING a DE 4 1 4 1 Query Capabilities cistitis ria 4 1 IMPORTANT INSTRUCTIONS AND FAQS Ne 5 1 5 1 Submission and Finalization process Nt 5 1 5 2 Regarding SOFT files and Zip afchiVeS cono nono ccoo conocio nre 5 2 5 3 Submitting the experiment to GEO nono nono nennen nennen 5 2 5 4 Updating the SOFT after
7. accession GSMxxx where GSMxxx indicates the accession number of the record to be updated similarly use Platform GEO accession GPLxxx and Series GEO accession GSExxx You can provide the entire SOFT record with the necessary revisions Alternatively you can simply provide the revised attributes and or data table Data table updates are all or nothing e g to revise data in one column of a table it is necessary to update the whole table Submit your SOFT update file by selecting the SOFT option on the Direct Deposit page Make sure to check the Update box Successful updates will be reflected immediately on your GEO records Refer the following examples data tables if any truncated at 20 rows for creating SOFT update files Anexample of a file updating Series attributes e example of a file updating an attribute in multiple Samples Anexample of a file updating data tables in multiple Samples Anexample of a file updating data tables and attributes in multiple Samples Anexample of a file updating Samples using complete SOFT records User s Manual Page 5 3
8. at is not listed please contact an administrator using the email address at the bottom of this page GEO Accession Number If your experiment has already been submitted and reviewed by NCBI GEO you can enter the GSM accession number associated with this particular chip here CEL File This drop down will contain a list of the CEL files you uploaded on the previous page Select the one for which you would like to add details CHP file This drop down will contain a list of the CHP files you uploaded on the previous page Select the one for which you would like to add details Factors Select the levels of the factors related to the chip you selected If you selected pig_4hours cel select 4 hours in the Time drop down menu here Organism Select the organism from which your sample came Organism part Enter the type of tissue from which the sample came Examples are liver lung MLN User s Manual Page 3 3 3 0 Using the System Sample molecule The molecule type extracted from the sample Labeling compound This is usually biotin for Affymetrix experiments In dual color experiments this is often or Cy5 Sample description A short description of this particular sample An example would be mesenteric lymph nodes non infected pig rep 1 Treatment protocol Describe the sample treatment You can find an example of this at this link Extract Scan Label Hybrid Protocols These drop down menus allow you to quickly s
9. elect a complete description of your protocol If you do not find your particular protocol in the list please contact us When you are done with that page you have several options a Cancel This will not submit your current hybridization and will bring you back to the main page b Save This will save the hybridization you are working on but will keep you on that page c Add another hybridization Saves your current hybridization and lets you add another d Save amp Continue If this is your last hybridization click this to save and move on to the last review step e Continue without Saving If this is your last hybridization click this to move on to the last review step without saving this hybridization 3 4 Review page This last page allows you to look at what you ve submitted and make sure it s correct When you are ready to submit click the Complete Submission button and it will be approved by an administrator before being submitted to the public database You should now see your experiment in the Your Submission table in Pending status User s Manual Page 3 4 4 0 Querying 4 0 QUERYING User s Manual 4 0 Querying 4 0 QUERYING The system can be queried using varied criteria on the search page http www anexdb org search php ANEXdb Search Microsoft Internet Explorer TER File Edit View Favorites Tools Help O
10. iew Favorites Tools Help a gt amp Pp Search Favorites O e a 3 Address E hipsffwnm anesch orafsubmkiuploachrhe _ Bo we Google G v Div Y Bookmarks Ehoblocked Y Check y y Autalink eb Send tov Settings Web Search S Bookmarks EMail Yahoo Edanswers Games Plantispyz News Sj shopping lt ANEXdb Submit Upload Add Tab A Please select all files related to the experiment and hybridizations and upload them here using this applet ANEXdb only supports files in Affymetrix formats CEL CHP or EXP On the following page you will associate these files with each hybridization filenames should therefore be unique so that you can distinguish files from one another Select Files to upload Browse Remove lear list Jpload MultiPowUpload 1 7 3 Y lt gt E Done internet 2 Start fm anexdb org default 3 anexdb org default Jaya anxdbojsrejed user manual Micros ANEXdb Help Mozill Z ANExdb Submit Up Once the plugin loads click Browse and select the CEL files and CHP files from your experiment You should probably have some way of identifying by the filename which chip it belongs to so that you can associate it on the next page When you are done selecting the files be sure to click the Upload button Once the upload is done move on to the next page User s Manual Page
11. itting sample information User s Manual Page 2 1 3 0 Getting Started 2 2 Dashboard After you register login using your email address and password After logging into the system the user will be presented with a dashboard where he can create new experiments ANEXdb Dashboard Mozilla Firefox TER File Edit History Bookmarks Tools Help E lt e a L http fww anexdb org dashboard php gt IG coco 2 Getting Started Latest Headlines svn cat ANEXdb Animal Expr 1 ANEXdb Animal Expression 4 1 ANEXdb Animal Expression ANEXdb Animal Expression L ANEXdb Animal Expression LJ ANEXdb Animal Expression Ly ANEXdb Dashboard agi ipi SS A N ANEXdb Animal Expression Database Dashboard Search Help Logged in as sushain pandit gmail com Logout ANEXdb gt Dashboard Your Groups Pm 1 Start New Submission croup name created E Lj You are not currently a member of any groups Your Submissions Your Account Info edit experiment date created status EFI You have no pending experiment submissions Email sushain pandit gmail com FirstName Sushain LastName Pandit Your Experiments JobTitle Graduate Research Assistant n Artificial Intelligence Research yet another test 2009 01 02 00 00 00 Public Lab another_test_2 2009 01 02 00 00 00 Public Insti
12. n This option can be used to search using any of the following Hybridization accession number ANX species GEO Sample Number GSM Sample description Sample tissue 4 1 4 Search by Gene or Sequence ID This option can be used to search using any of the following Gene Name Affymetrix Id NCBI RefSeq ID 4 1 5 Search by Affymetrix Probe ID This option can be used to search using affymetrix probe id For instance Ssc 10082 1 A1_at 4 1 6 Browse by Organism This option can be used to search using any of the organism types using the drop down menu given User s Manual 4 0 Querying 5 0 IMPORTANT INSTRUCTIONS AND FAQS User s Manual 5 0 Important Instructions and FAQs 5 0 IMPORTANT INSTRUCTIONS AND FAQS This section contains some important observations that may come handy to the users 5 1 Submission and Finalization process Once an experiment is submitted it is temporarily stored in an intermediate database and remains there until the admin finalizes it The finalization process is essentially controlled by the system admin and it is his responsibility to ensure that the experiment submission is proper and in accordance to guidelines however to make his job easier it is recommended that submissions be made as per the above specified guidelines Once the experiment gets finalized it is queued and gets processed within a pre determined time slot by a server based cron process This pr
13. ocess runs 12 am 7 am due to server load constraints and thus it is not recommended to browse click review your experiment until a day after it is finalized and appears in the Search Results This will ensure that the data has been processed and the soft files will be properly generated Failure to conform with the above guideline will result in incorrectly populated soft file references Once the experiment is finalized can be viewed in the Search Results and the above mentioned time period has elapsed one may go ahead and click on the corresponding experiment on the search page 2 ANEXdb Search Results Mozilla Firefox Elle Edit view History Bookmarks Tools Help gt L1 http llwww anexdb orglquerylresuks php z gt Getting Started Latest Headlines svn cat ANEXdb Animal Expr 9 D p ANEXdb Animal Expression Database L ANEXdb Animal Expression Database ANExdb Animal Expression Database L ANEXdb Animal Expression Database ANEXdb Search Results B eXalo ANEXdb Animal Expression Database Home Dashboard Search Help Logged in as sushain pandit gmail com Logout ANEXdb gt Search gt Results Search Results ni CO DS INN yet_another_test Bos taurus Sushain Pandit 2009 01 02 00 00 00 another_test_2 Ovis aries Sushain Pandit 2009 01 02 00 00 00 testing_multiple_hybrids Homo sapiens Sushain Pandit 2009 01 02
14. the experiment submission and you should either change it to the correct value manually or re submit the experiment with the correct value files The zip archive would contain soft cel chp files for the experiment submission All these would be needed since soft refer to them and they re all needed to conform to GEO submission requirements It is highly recommended to cross check the zip contents before submitting it to GEO In case any of the experiment related files cel chp is found missing you should either manually add it to the archive or check your experiment submission on the experiments page to ensure that you indeed submitted the file during the submission process If you find that the file is absent in the zip even though it appears in the submission please drop a note to one of the points of contact refer 1 4 5 3 Submitting the experiment to GEO For successful submission to GEO one would need to submit a zip archive of the generated SOFT file and the CEL CHP files using the Direct deposit option at the Direct Deposit page Select File format SOFT Submission kind new and enter an appropriate Release date for your data before clicking the Submit button User s Manual Page 5 2 5 0 Important Instructions and FAQs 5 4 Updating the soft after submission if required For performing batch updates in the submitted SOFT follow these guidelines Include the attribute Sample GEO
15. tution Iowa State University testing multiple hybrids 2009 01 02 00 00 00 Public Street testing new jar 2009 01 02 00 00 00 Public State City Country Zip Phone 515 451 0757 v Done start anexdb org default I anexdb org default Java srejec Uy user manual Micros ANEXdb Dashboard 2 2 4 Start New Submission This may be used to start the new submission Click on the Start New Submission link to begin entering a new experiment 2 2 4 Your Submissions Experiments These boxes enlist all the submissions done under one particular used id along with other useful information on the current status of submissions 2 2 1 Account Info Groups User s Manual Page 2 2 3 0 Getting Started These enlist your profile information and whether you ve any group privileges as determined by the ANEXdb admin 2 3 Exiting the System Make sure you logout properly by clicking logout on the top right Any incomplete submissions can be located within Your Submissions box when you log into the system the next time User s Manual Page 2 3 3 0 Using the System 3 0 USING THE SYSTEM User s Manual 3 0 Using the System 3 0 USING THE SYSTEM 3 1 Submitting an experiment Clicking Start New Submission on your dashboard starts a new experiment 2 ANEXdb Submit Experiment Mozilla Firefox File View History Bookmarks Tools gt L1 http lwww anexdb orglsubmi e
16. w O 8 0 Ds dim O 2 5 m 5 Address http laww anexdb orgjsearch php _ Bo Google G v Div Y Bookmarks Ehoblocked Check y y Autolink 1 Send tow Q Settings Y _ Cy Web Search Ep Bookmarks Fisettings E mal gt Yahoo EQ answers Q Games blanti spyz EpNews 1 shopping QS anexdb Search Add Tab ANEXdb Animal Expression Database Dashboard Search Help Logged in as sushain pandit gmail com Logout ANEXdb gt Search Search by Experiment Search by Consensus ID Se er ANX species amp owed by Contig number E Search by Gene or Sequence ID Find by Gene Name ie CoA g Search by Affymetrix Probe ID Browse by Organism Ee 1 go Return all experiments from the following species Select an Organism vL Y lt a El Done Internet 1 start fa anexdb org default 3 anexdb org default ava ai x Ty user manual Micros ANEXdh Help Mozil Z ANEXdb Search Mi 4 1 Query Capabilities 4 1 1 Search by Experiment This option can be used to search using any of the following Experiment Accession number ANX species Experiment title keywords GEO Data Set or Series GDS GSE 4 1 2 Search by Consensus ID This option can be used to search using Enter Cluster number followed by Contig number i e ITC 1 1 GEO Data Set or Series GDS GSE User s Manual 4 0 Querying 4 1 3 Search by Hybridizatio
17. xperiment php new 1 MW Getting Started Latest Headlines svn cat ANEXdb Animal Expr ANEXdb Animal Expression ANEXdb Animal Expression 1 ANEXdb Animal Expression 1 ANEXdb Animal Expression 1 ANEXdb Animal Expression Lj ANEXdb Submit Experi E Experiment ANEXdb follows the guildlines for a GEO SOFT submission For a full description go here Experiment Title Experiment Description Visibility Public Group optional Selecta group for group visibility GEO Accession Number gt GSE or GDS 7 Experiment Design Factor 1 Number of Levels Add Factor Refresh Factors Factors should include every factor relevant to the study Experimental conditions such as time points animal lines administration of a drug and dose Animal specific items such as animal numbers Replicate information for either biological or technical replicates Done 2 start f anexdb org default 8 anexdb org default Java anxdho srcfec Uy user manual Micros ANEXdb Submit E Following is a general guideline for experiment submissions Title The experiment title is the same as what you would see in GEO An example would be Expression data from non infected and Salmonella Typhimurium infected mesenteric lymph nodes Description This is a longer text description of the experiment and its design You should probably mention
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