Tissue Manual | Cataloging Tissues
Basic Guidelines for Cataloging Tissues
Assume that tissues exist for an accession unless told otherwise by the collector or donor. Data on tissues should be obtained from the field/prep catalog. However, because collectors/preparators may be inconsistent in annotating tissue information, tissues should be inventoried before adding them in Arctos.
All tissues should be cataloged at the same time as voucher specimens. If the accession includes a mixture of MVZ-vouchered and non-vouchered tissues (including vouchers deposited in another institution), the non-vouchered tissues should be integrated with the vouchered material when cataloging.
Tissues are treated like any other specimen part when cataloging. Tissues may be added either in the Arctos data entry screen (before the data have been loaded), in a bulkloader spreadsheet, or after the data have been loaded.
The first step in cataloging tissues is to find their location. The procedure will differ by collection depending on how uncataloged tissues are tracked (see Tracking Uncataloged Tissues). To search for tissue locations in Arctos, you will need manage_container permission. Once logged in, go to Manage Data —> Object Tracking —> Find Container. You can either search by the barcode or label associated with a vial or freezer box.
If the data have been loaded into Arctos and you only know the MVZ catalog number or the accession number, you will need to find the collector/preparator information first. Go to Search —> Catalog Records, select the collection from the dropdown (e.g., MVZ Bird Specimens), and enter either the MVZ # in the “Catalog Number” field, or the accession number in the “Accession” field (tip: precede the accession number by an equal sign for faster searching, e.g,. “=15466”). Use the initials for the collector/preparator in your object tracking search.
Example of searching for a tissue vial by collector/preparator initials and number.
Enter the initials and number (e.g., CC 4300) in the label field. The results (right side of screen) show two tissue vials for that specimen (barcodes MVZ238128 and MVZ238129). The first is in position 45 in a freezer box located in Freezer 2, Section F, Rack 55, Slot 3. The second is in position 3 in a freezer box located in Freezer 2, Section F, Rack 55, Slot 5.
Example of searching for a tissue box by the description:
Enter the description in the label field, using the wildcard symbol “%” as needed (e.g., %mcguire%2010%). The results (right side of screen) show nine boxes in Freezer 1, Section G, Rack 46, Slots 1-8 and 13.
Adding Tissues in Data Entry
Enter “tissue” as a part name, press tab, then select the preservation method from the drop-down list.
The default condition is “unchecked” but enter something else if applicable (e.g., “tissue possibly degraded”).
The default disposition is “in collection” but enter something else if applicable (e.g., “missing” if tissue was reportedly collected but could not be found when cataloging).
The default count (#) is 1. Leave that as is. If multiple tissue vials were saved, each vial should be entered as an individual part because it can be tracked separately using the barcode.
Scan the barcode from the vial using one of the scanners available in the liquid nitrogen room. Always make sure that the barcode scans correctly (i.e., that “MVZ” precedes the number). This step can be done after the initial data entry, if it’s easier to first enter the specimen data in the main curatorial work area and then handle all of the tissues at once.
Enter the tissue type(s) in the remarks field, or any other remark such as information about the tissue disposition if not in the collection.
Adding Tissues in the Bulkloader
Bulkloader spreadsheets are useful when cataloging accessions with more than 20-30 specimens. Bulkloader templates can be built and downloaded from Arctos (Enter Data –> Bulkloader –> Bulkloader Builder).
If there are multiple tissue parts for a specimen, repeat the set of columns but change the headings to be PART_NAME_2, PART_CONDITION_2, PART_LOT_COUNT_2, PART_DISPOSITION_2, PART_BARCODE_2, PART_REMARK_2, and repeat as necessary for more parts by incrementing the number to reflect the number of parts
PART_NAME_1 = “tissue (frozen)”
PART_CONDITION_1= “unchecked” (default) or “tissue degraded” (or some other condition) if noted by the preparator
PART_LOT_1 = “1” (if there are >1 vials, create a new part for each one)
PART_DISPOSITION_1 = “in collection” (or “missing” if not found, “discarded” if thrown way, etc.)
PART_REMARK_1 = “Heart, liver, muscle, kidney.” (or whatever the tissue type is indicated for that vial)
Adding Tissues by Editing Parts
If the data have been loaded into Arctos, then tissues must be entered by editing the parts in the specimen detail page.
Search on the accession in Arctos to get a list of specimens (Search —> Catalog Records —> Accession), or search directly for the specimen you want to edit (Search —> Catalog Records —> Catalog Number). Click on the MVZ number to get into the specimen detail page.
On the right side of the screen in the Parts box, click ‘edit’ to get to the editing screen.
If a tissue part already exists in Arctos, but without the barcode, skip to step 10 below.
If you need to add a new part, go to “Add Specimen Part” and enter ’tissue’ in the Part Name field and hit the tab key. This will provide a pop-up window with different tissue part options from the controlled vocabulary. Select the part that matches the tissue you are cataloging, e.g., ’tissue (frozen)’ or ’tissue (RNAlater).’
In the count field, enter one (1). If you have more than one tissue vial for a specimen, enter each one as a separate part. This is important because each vial has its own barcoded and can be tracked separately for loans.
In the disposition field, enter ‘in collection.’ If there is supposed to be a tissue according to the original data, but you cannot find it, enter ‘missing’ to track that one existed at some point.
In the condition field (required), enter ‘unchecked’ unless the preparator noted something about the tissue, e.g., ’tissue degraded’ in which case enter that. Enter condition in lower case.
Remarks can be used to make a comment about the tissue, e.g., if disposition is missing, enter something about when it was found to be missing (‘Tissue not found when cataloging specimen May 2020.’). Enter the remark as a sentence, starting with a capital letter and ending with a period.
Scan the barcode on the tissue vial into the ‘AddToContainerBarcode’ field (or if the tissue part has already been created, into the ‘Add to barcode’ field. Make sure that when you scan the tissue barcode, it scans properly with the number preceded by ‘MVZ’ with no space. This is very important because if scanned improperly, the barcode may be affiliated with a different collection in Arctos.
Hit “Create” to save the new part.