Epigenomics User Workflow Document- Internal Users

Transcription

1 Epigenomics User Workflow Document- Internal Users Create a Request in ilab: Two options are available: i. Consultation: choose this option to schedule the initial consultation (included in our services), in order to discuss the best options for your project. ii. Project request: chose this option if you know the specific assay(s) you want done on your samples (usually after the initial consultation was conducted). In either case, you need to follow steps 1-7 below: 1. Navigate to the core page: 2. In the upper- right- hand corner of the screen click the green Login button Login bu)on

2 3. Under UMich user click here to be redirected to the authentication page Click on this link to login 4. Enter your UMich ID and password, and sign in.

3 5. Once you login to the URL above, your account will open to the View My Requests Tab. 6. Select the Request Services tab Request services tab

4 Create a consultation request in ilabs 1. Once in the Request service tab, click on the button to the right of the Consultation section. Click this bu,on to schedule a consulta)on 2. The figure below shows the Consultation request form to be completed. Once completed, you can submit it to the core.

5 3. Submit the request to the core. The status of your request will be in Waiting for Core to Agree. 4. Your request will be pending review by the core. The core will review your request and either Agree to the work or they will ask for more information if needed. 5. Once the core agrees, the status of your request changes to Waiting for Researcher to Agree. You will receive an notifying you of the need to login to ilab and agree to the request. Create a Service request in ilabs 1. To start the sample submission for your project, click on the Request Service button on the far right of the Project Request section.

6 2. You will be asked to complete a form before submitting the request to the core. This form has multiple parts that must be filled before request submission: I. Project Information: Person doing the submission. Can be the PI address Briefly explain (1-2 sentences) the purpose of the study. This number can be # samples in first submission This requires an addi-onal consulta-on. No-fy us ASAP if it was not done at your first contact with our Core II. General Sample information for the entire project In this section, you give the core a general overview of your project: what type of sample you are submitting, what assay you are requesting and the number of samples for each assay. Use the grey arrow on the right of each box to select the Sample Type and Assay Type you want. You will provide detailed information for your samples in the next section.

7 Depending on your project, you may be requesting only one or more assays, on all/some of your samples. Two examples are provided below. Example of the Sample information table for a simple project: Example of the sample information table for a complex project: The 5hMeDIP is required on 5 of the 10 samples submi;ed III. Sample Information for samples submitted This is the section where you provide detailed information on each sample you are submitting. For some project, you may be submitting samples at different times (example: clinical samples). You will be able to return to the service request when you are ready to submit additional samples.

8 total number of samples in the project Form to be completed and uploaded with you service request This part is to be used only if you are submi;ng addi=onal samples to an already exis=ng project Irrespective whether it is a single submission, or the first of many submissions, they all require the UMich_Epigenomics_Sample_Template- 2.xlsx file to be completed and uploaded with your project. Failure to fill this spreadsheet will result in delays for processing your project request/samples. The image below shows the top part of the excel spreadsheet that is to be submitted with your project request Below is a brief description of each column of the excel spreadsheet Sample Number : general numbering of the lines in the spreadsheet Sample Name (from researcher): Name you put on the eppendorf containing the sample. Sample Type (DNA, RNA, cells): whether the sample is DNA, RNA or Cells DNA/RNA Concentration Method (nanodrop or picogreen): How you quantified the sample concentration DNA/RNA Concentration (ng/ul): concentration obtained with the method in the previous column. DAN/RNA Total Volume (ul): volume you are sending to the Core

9 DNA/RNA Buffer type: what is your DNA/RNA is resuspended in Total cell number: How many cells in the vial ; If you are submitting cells only. Assay type: WGBS=1; ERRBS=2, merrbs=3, illumina 450k=4, MassArray=5, Pyrosequencing=6, medip=seq=7, 5hmeDIP- Seq=8, CHIPseq=9 Sequencer: Type of Illumina sequencer (HiSeq2500 or HiSeq4000). This is especially important for projects with multiple sample submissions, or legacy projects (where first samples were sequenced on older machines). PE or SE: Paired- End or Single- End Read length (50 or 125): how many sequencing cycles For ChIP- seq ONLY: Ab choice: If you are submitting samples for ChIP- Seq, you need to indicate which Antibody is to be used for chromatin pull- down (this will have been determined/discussed at the consultation stage). 3. Submit the request to the core. The status of your request will be in Waiting for Core to Agree. 4. Your request will be pending review by the core. The core will review your request and either Agree to the work or they will ask for more information if needed. 5. Once the core agrees, the status of your request changes to Waiting for Researcher to Agree. You will receive an notifying you of the need to login to ilab and agree to the request.

10 Here is an example of the you will receive to notify you the core has agreed to the request: Here is an example of the view you will see in the View All Requests Tab. 6. If you agree to the total proposed cost the status changes to Waiting for Core to Begin. At this point you will be able to track the status of the request in ilab. The core will begin the request and the status will change to

11 Processing. Once the core completes the work, the status will change to Complete. You may receive an notifying you that work is complete. Other times you may receive an 1. The core makes a comment on the request or replies to a comment you left.

12 2. Your request has been completed.