Sample Submission
woman in lab holding advanced genomics technology

General information for recommended input requirements and instructions for submitting samples, based on sample types.

NGS, Genotyping, and QC
Input Requirements

The Advanced Genomics Core prefers >200 ng for most assays. The higher input yields better performing assays and more robust data.

Illumina AssayMin Recommended InputMin VolumeQuality and Concentration Minimums
Poly-A (standard) Library Prep50 ng25 µlRIN > 7 and 2 ng/µl
Poly-A (low input) Library Prep1 ng25 µlRIN > 7 and 0.05 ng/µl
Total RNA* (standard) Library Prep100-400 ng15 µl

DV200 >70%  – 6.6 ng/µl (100 ng total)

DV200 50-70% – 13.3 ng/µl (200 ng total)

DV200 30-50% – 26.7 ng/µl (400 ng total)

DV200 < 30% not recommended

Total RNA* (low input) Library Prep1-4 ng15 µl

DV200 >70%  – 0.06 ng/µl (100 ng total)

DV200 50-70% – 0.13 ng/µl (200 ng total)

DV200 30-50% – 0.27 ng/µl (400 ng total)

DV200 < 30% not recommended

small RNA Library Prep10 ng15 µlif submitting total RNA RIN > 7
DNA (standard) Library Prep100 ng25 µl4 ng/µl
DNA (low input) Library Prep0.5 ng25 µl0.02 ng/µl
User-made Library10nM25 µl< 1% adapter dimer

*The ribosomal depletion probes used during Total RNA library prep are selected based on the species indicated in the submission form. If both bacterial and human/mouse/rat probes are required, you must include both species in your form or indicate that it is mixed species. If your samples are isolated from blood and you require globin depletion, please indicate that in the submission notes.

Preferred Buffers:

  • RNA (DNase treated) – molecular biology grade water (NOT DEPC)
  • DNA – EB buffer (10mM TRIS (pH= 8.0-8.4)) or molecular biology grade water 
  • Illumina Libraries – EBT (10mM TRIS + 0.1%Tween20), EB (10mM TRIS)

Note: The presence of EDTA can inhibit enzymatic activity and lead to reduced final yield, failure of library prep, or low and uneven coverage when analyzed bioinformatically.

Oxford Nanopore library preparation is sensitive to contaminants that can be revealed by Nanodrop readings. Note that the rapid chemistry is optimized for samples >30kb, while ligation sequencing can accommodate both HMW DNA and amplicons.

ONT AssayRecommended InputMin ConcentrationMin VolumeQuality
Ligation Sequencing (with or without Native Barcoding)1-2µg25 ng/µl30-50 µl260/280 ~1.8-2.0
260/230 ~2.0-2.2
Rapid Barcoding Sequencing500ng (≤12 samples)
100ng (>12 samples)
55 ng/µl (≤12 samples)
6 ng/µl (>12 samples)
10-15 µl260/280 ~1.8-2.0
260/230 ~2.0-2.2

Preferred Buffers:

  • 10 mM TRIS (pH=8.0-8.4)

Note: We require that you provide us with a minimum 20ul aliquot of your elution buffer, so that we can use it to get accurate nanodrop readings when assessing the purity of your samples. This aliquot should be labeled with your Service Request ID and “EB”.

Other AssayMin Recommended InputMin Volume
Quality ControlNA5 µl*
BeadArray Genotyping500 ng10-15 µl

*** note if less than 5 µl is provided, water will be added to your samples to bring the volume to 5 µl ***

Preferred Buffers:

  • 10x Genomics – 1X PBS (calcium and magnesium free) containing 0.04% weight/volume BSA (400 μg/ml). If necessary, PBS can be replaced with most common cell culture buffers.

Note: Nanodrop can overestimate the amount of nucleic acid in a sample since it is not DNA/RNA-specific and can be influenced by the presence of contaminants. Fluorescence-based concentrations can be as much as 50% lower than those determined by nanodrop. If using nanodrop to quantify your samples prior to submitting to the AGC, be sure to at least double the amount of material being submitted.

Preparing Samples for Submission

The AGC accepts aliquots in either tubes or plates. You must select either tubes or plates when you create your Service Request in MiCores. You can use either plates or tubes, as you prefer. We recommend using a plate when you have more than 7 aliquots in your submission. When submitting samples in plates, please use 96-well, skirted PCR plates.

Once your Service Request has been accepted by the core, you will get an email with the  Core Sample Ids or Core Plate Ids. You must label your tubes, plates, and bag with these numbers or your submission will be returned to you.

You should print out the PDF attachments from your acceptance email from the Core. You will need it for labeling, and you can then put it inside your submission bag.

You selected tubes or plates when you created your submission in MiCores. Detailed instructions for each are below.

Remember: Do not submit your entire sample. The AGC does not return unused aliquots.

1A) Preparing Tubes

  1. Aliquot your samples into 1.5 ml tubes.
  2. Securely close the tube caps.
  3. Make sure that Core Sample Id numbers are clearly written on the top of each tube. Like this:
    close up example of how to write a core sample ID
  4. See below for instructions on putting your samples into a plastic zip-top bag and getting them to the Core.

1B) Preparing Plates

  1. If submitting samples in plates, use 96-well, skirted PCR plates. Skirted plates help prevent bending, which can lead to leakage, during transit. The plates should be sealed with a foil cover capable of withstanding -80°C temperatures.
    • Product Examples
      • Plates:
        • VWR #83007-374 VWR 96-Well PCR and Real Time PCR Plates; Half-skirt
        • VWR #82006-704 VWR 96-Well PCR and Real Time PCR Plates; skirted
        • Eppendorf #30129504 Eppendorf twin.tec PCR Plate 96 LoBind, semi-skirted, PCR clean
    • Seals:
      • VWR #30623-776 AlumaSeal 96 Sealing Foil (EXCEL), Nonsterile
      • Corning #6570 Corning 96-well Microplate Aluminum Sealing Tape, Nonsterile
  2. Aliquot your samples into plates using the plate map included in the acceptance email from the Core.
  3. Note that your samples will be be arranged vertically (in columns) as shown here:
    example of a plate map
  4. Follow the instructions below on putting your samples into a plastic zip-top bag and getting them to the Core.
  1. Using a zip-top bag that you supply, write the Submission Id on the bag in permanent waterproof pen.
  2. Place all tubes or plates into the zip-top bag.
  3. Place your printed attachments inside the bag.
example of the submission instructions on the aliquots bag
NGS, Genotyping, QC, & QPCR Samples

Do NOT place dry ice in the drop-off freezers. Samples submitted to the remote freezer locations (MSRBII C555 and NCRC Dock) are couriered to the AGC on dry ice M-F afternoons.

If the drop-off locations at MSRB II or NCRC014-122 are closed because of a weather incident, you can still drop off samples at NCRC Building 90 Dock (details below) daily between 7am and 4:30pm, as long as NCRC is open.

Sample drop-off is contactless. Drop-off instructions depend on the submission location:

Drop-Off Locations

If you work in the MSB complex, you can drop samples off in our MSRB II C555 location.

The MSRB II C555 (equipment corridor) location is accessible 24/7.

on-location image of MSRB II C555 (EQUIPMENT CORRIDOR)

 

  1. IMPORTANT: You must first aliquot your samples and bag them. See sample preparation instructions for more information.
    example of the submission instructions on the aliquots bag
  2. Bring the appropriately bagged aliquots to MSRB II, C555.
  3. Put the bagged/boxed samples in the large “Advanced Genomics Core Sample Submission Freezer” in one of the metal baskets. Please note that you no longer need to enter info into a sample drop-off log.
    on-location image of Sample Submission Freezer
  4. A courier transports samples from MSRB to the AGC on dry ice most weekdays at about 2:00 pm. Note that the exact date and time may change because of weather and other external factors.
  5. When the core receives your bag, you will get an email notification from our system.
    screenshot of example email notification

If you have questions, fill out our online Consultation Request Form.

If you work in U-M buildings other than the NCRC or MSRB complexes, or the AGC drop-off locations in NCRC Building 14 or MSRB are closed for a weather emergency, you can drop your samples at the NCRC dock (building 90).

NCRC Building 90 Dock is open workdays, 7:00am to 4:30pm.

Watch a video of how to find NCRC Building 90 dock.

  1. IMPORTANT: You must first aliquot your samples and bag them. See sample preparation instructions for more information.
    example of the submission instructions on the aliquots bag
  2. Bring the appropriately bagged/boxed samples to the NCRC dock located in building 90. Watch a video to see how to find NCRC 90 Dock.
    map of NCRC campus labeled with instructions to Dock
    aerial photo of the NCRC Dock
  3. Enter via the B90 NE Exterior door leading to the dock GSS Security station.
    NCRC Building 90 NE exterior door
  4. Place the bagged/boxed samples in the freezer labeled AGC Sample Submission Freezer.
    on-location image of Sample Submission Freezer

The drop off location will be accessible 7:00am – 4:30pm, Monday – Friday. Samples are transported on dry ice to the AGC daily.

If you have questions, fill out our online Consultation Request Form.

If you have access to NCRC Building 14, you can submit samples directly to the core.

  1. IMPORTANT: You must first aliquot your samples and bag them. See sample preparation instructions for more information.
    example of the submission instructions on the aliquots bag
  2. Bring samples and submission paperwork to the AGC drop-off window (NCRC Building 14, Room 122).
    AGC drop-off window in NCRC Building 14, Room 122
  3. Following instructions on the freezer, place samples in the appropriate location.
    Sample Submission Freezer Instructions
  4. When the core processes your bag, you will get an email notification from our system.
    screenshot of example email notification

If you have questions, fill out our online Consultation Request Form.

If you do not have access to NCRC Building 14 or MSRB II

Customers who do not have access to NCRC or MSRB can either ship their samples to us, or drop them off at a freezer at the dock in NCRC Building 90.

  • IMPORTANT: You must first aliquot your samples and bag them. See sample preparation instructions for more information.
  • To drop off at the dock at NCRC Building 90 (follow the instructions above). We also created a video to help you find the dock at building 90.
  • To ship your samples to us, send them to:

U-M Advanced Genomics Core
NCRC Building 14 Rm 122
University of Michigan
2800 Plymouth Rd
Ann Arbor, MI 48109-2800
Phone: 734-764-8068

Single Cell Spatial Omics
Input Requirements
Assay Buffer Amount
10X Genomics 3', 5' or Immune Profiling Most standard medias with no more than 2% BSA, 10% FBS, and no EDTA 50K cells in 40-50ul buffer
10X Genomics ATAC or Multiome (GEX+ATAC) 10X Genomics Nuclei Buffer* 50K nuclei in 10-20ul buffer
10X Genomics Single Cell RNA Flex 10X Genomics Quenching/Resuspension Buffer* 50K cells or 5-50mg tissue
ParseBiosciences EverCode Parse Biosciences fixation solution* 100K cells
Direct Cell Lysis Vendor provided buffer in 96-well plate* Full 96-well plate

*These buffers can be picked up/purchased from AGC

Assay Slide Type Thickness
10X Genomics CytAssist Charged glass slide 5um FFPE; 10um Frozen
Nanostring GeoMx DSP Charged glass slide 5um FFPE; 10um Frozen
Curio Biosciences CurioSeeker CurioSeeker Tile* 10um Fresh Frozen
10X Genomics Xenium Xenium slide* 5um FFPE; 10um Frozen

*These can picked picked up/purchased from or sectioned by AGC

Preparing Samples for Submission

Make your appointment via the AGC MiCores site – “Schedule Equipment” -> “Single Cell Appointment Request”

screenshot of options in MiCores, highlighting "Schedule Equipment"
screenshot of options in MiCores, highlighting "Single Cell Appointment Request"

 

You may select any time within the blue boxes. If you have fewer than 6 samples, a 30 minute time slot is sufficient.

screenshot of options in MiCores, highlighting "Select a Time"

 

Fill out the form. We have a large number of options, so please look them over carefully. Viability/Count checks can be found under the “10X Genomics” options. Please note the “Comments” tab at the top – if you need to cancel your appointment after it has been confirmed, or anything else comes up, you can use this tab to communicate with us.

screenshot of options in MiCores, highlighting appointment details

 

Submit your service request on the AGC MiCores site – “Request Services” -> “Single Cell Processing.” This MUST be done before you bring your cells to the Core. Most people fill out their service request 2-24 hours before their appointment time. If you have not created a service request before bringing your cells, we cannot accept them.

screenshot of options in MiCores, highlighting "Submit your service request"

 

The request form will ask you for your analysis type, read depth (sequencing depth), targeted number of cells (1,000-10,000), and your sample names. When that has been submitted, you will receive an email with the numbers that correspond to each sample. Write your sample numbers on the top of your sample tubes. If your sample numbers are not on the tops of your tubes, we cannot accept them.

close up example of how to write a core sample ID

 

Package your samples in either a plastic bag or 50ml conical tube, then inside a cooler on ice. If your samples are not in an appropriate secondary container, we cannot accept them. This protects both you and our technicians, and is mandated by EHS. Pictures of two acceptable submissions are below.

samples labeled with appropriate packaging

 

Come to NCRC. Guest services is now staffing the lobbies at both Building 18 and Building 32. Show your MCard to gain access. You will then need to make your way to the lab in Building 14. Note that the most direct path through the complex is to enter through Building 32.

map of NCRC campus labeled with instructions to AGC

 

Ring the Single Cell and Spatial doorbell when you arrive. We will take your samples and check the concentration and viability while you wait. We will discuss the results with you so that you can make any decisions to proceed immediately.

Walk up the extremely long walkway to the door to Building 32. Head to the right and show your MCard to the Guest Services agent. Through the lobby, turn left down the long hallway. You will pass the 24/7 Market and walk up one small set of stairs.

on-location images of the hallways leading to AGC

 

Walk straight until you reach the courtyard. Turn left. Walk straight until you have entered Building 14. Once you see the recycling gondola, look to your right. AGC Single Cell and Spatial drop-off is at Room 171. Ring the doorbell and someone will be with you shortly.

on-location images of the hallways leading to AGC
Drop-Off Instructions
  • Appointments are required to submit single cell or spatial samples. Reservations are made via MiCores.
  • Submission: Samples should be placed in a secondary container, e.g. a small plastic biohazard bag, for transport to the AGC.
Questions?
Contact Us
Room 122
NCRC Building 14
University of Michigan
2800 Plymouth Rd.
Ann Arbor, MI 48109-2800
About Us
The Advanced Genomics Core is one of the Biomedical Research Core Facilities, and a part of the Medical School Office of Research, where our mission is to foster an environment of innovation and efficiency that serves the Michigan Medicine research community and supports biomedical science from insight to impact.