Sample submission guide
- Gregg Randolph
- Shannon Harris
General guidance
On campus drop-off should be arranged ahead of time with the GTL Lab Manager Gregg Randolph via e-mail. Typically, arrangements for drop off should be possible M-F 10-4 PM. Samples can be provided in 96-well plates or microcentrifuge tubes. At this time we are not accepting 384-well plates.
If nucleic acid extraction services are required, then special arrangements can be made to drop off tissue samples. All samples must be clearly labeled following guidelines provided below. For UWYO EPSCoR clients (henceforth referred to as “internal clients”), samples should have metadata uploaded to the LIMS prior to sample submission to the Genome Technologies Laboratory. Clients that are not a part of the EPSCoR funded microbial ecology collaborative are referred to as “external clients” in this document.
Samples should be arrayed in plates or tube racks such that columns are filled, rather than filling rows of the plate. To be clear, the first eight samples would be placed in the first column of the plate or rack (A1-H1), then the second eight samples added to the second column, and so on. This makes it much easier for us to pipette samples. We will not accept samples that are improperly arrayed. This is so we do not rearrange your samples, potentially causing errors when assigning samples to wells.
DNAs should be added to each well in 30 ul aliquots. DNA should be suspended in either TE or elution buffer from Qiagen kits. If DNA is suspended in some other buffer or solvent be sure to mention this to Gregg Randolph as it could have critical effects on library preparation success. Submission of 20 ul aliquots is acceptable if every sample provided is 20 ul. If 20 ul is provided, samples must be clearly marked to let the GTL know that less volume has been provided than is typical.
Samples can be dropped off outside Berry Center 320, the Genome Technologies Laboratory. There is a small -20 C Freezer labeled “GTL DropOff Freezer”. Samples must be labeled clearly, have a date, client, and project name placed on them. Samples can be dropped off in it and an email should be sent to gtl@uwyo.edu with one of the forms below attached.
Submission Forms
GTL Tube Submission Form (81 Sample Box)
GTL Plate or Tube Submission Form (96 Well Format)
UWyo EPSCoR Micro Submission Forms
EPSCoR Tube Submission Form (81 Sample Box)
EPSCoR Tube Submission Form (96 Well Format)
To better assist you with filling out the submission forms, a tab labelled “!QuickTips” is located in each form with instructions and explanations for each column.
Sample submission
Submission vessel and LIMS barcode application
Plate submission
Plates are the preferred vessel for sample submission.
Samples should be added to the plate column-wise. Start with A1, B1, C1, D1, E1, F1, G1, and H1 before adding to the second column. We will not accept plates that have been filled row wise (e.g., all of of row A filled but all other rows empty), because we will have to rearrange those samples and this could lead to errors when linking sample to well.
Partial columns should be filled with TE blanks. Remember to include these blanks in the above forms. If you are an internal client and do not have TE, talk to Gregg Randolph about having the GTL add TE.
Fully empty columns should be left empty.
The key matching sample to well position should be provided. Ensure that this key proceeds column-wise (see general guidance above), otherwise several of our sample processing scripts will not work as expected.
Plates should be labelled (LIMS barcodes) on the lettered side of the plate at the least.
Tube submission
Non-University of Wyoming clients with more than 16 samples must submit samples in plates.
If more than 16 samples are to be submitted, then these should be placed in 96 tube racks (8x12) with the layout provided matching the desired sample to well relationship. Samples should be added column-wise (A1, B1, …H1 should be filled prior to moving to the second column). This allows us to quickly move samples from tubes to plates, while preserving the desired sample-well relationship.
For EPSCoR UWYO clients, barcodes must be placed parallel to the long-axis of the tube, so that barcodes are not wrapped around the tube. This makes it easier to scan barcodes.
Labeling conventions
Consistent labeling of samples is critical for us getting your data processed effectively. Improper labeling can cause loss of sample data during bioinformatics, thus all samples submitted to the GTL will adhere to the following labeling conventions.
Sample names
Sample names may not contain periods, commas, hyphens, any of the following symbols {}~`!@#$%^&*()+=[]|\/?>< or any white space characters. Sample names may contain underscores, as well as numbers and letters. Vsearch does not handle hyphens well so please avoid these at this time. Sample names may start with a number (e.g., 1_1_1_3), however be advised that, depending upon downstream analyses you may run into unforeseen issues with such names. R for instance, often will put an X in front of strings starting with numbers that are specified as field names. If only a few of your samples start with a number, then it is easy to accidentally omit them during some later analysis. If you keep this limitation in mind, then starting names with numbers is ok.
Our bioinformatics pipeline will treat each MID combination as a separate sample, even if multiple samples have the same sample name. This means that sample replicates can be merged subsequently, but that our bioinformatics will treat them as separate.
Examples of useful and acceptable sample names:
asle_plant_1
snowrangedirtclod_2
These sample names should be linked to wells in the 96-well plate provided via a key that is backed up in several places and, if on-campus, stored in the LIMS.
LIMS details and tutorial
For internal clients, under development
Expected deliverables
Clients can expect fastq files for each sample submitted. The file name will include the client name, project, sample name, substrate, and locus sequenced. All of these items will be separated by periods. For instance, a file name may look like this: harrison.asle.plant_number1.plant.16s.fastq
Data for external clients will be provided via methods agreed upon by the client and Gregg Randolph prior to project initiation. For example, data could be uploaded to a portable hard drive or placed in a ftp/scp accessible location, depending upon client preferences.
Data for internal clients will be stored on Teton at /projects/microbiomes/data/seq/directoryforsequencingrun The exact directory will be provided to the client. These data should be read from this location, but output and further analyses should go in /projects/microbiomes/analyses/ or temporarily in /lscratch or /gscratch directories.
A “parse report” for the entire sequencing run, along with diagnostic summary statistics from the sequencing provider will be available for the entire sequencing run. If clients desire this information then it can be provided, though in most cases it should provide little value to clients and is mostly useful for us here at the GTL.
Additionally, some samples in each run will be controls included by the GTL. These samples will be clearly marked as XXXX (under development) and available for download by all clients whose samples were sequenced on that run.