This BrianCottle_readme20191113.txt file was generated on 20191113 by Brian Cottle Links to Publication Field updated. 2021-12-09, SES ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data for: Localization of the Sinoatrial and Atrioventricular Nodal Region in Neonatal and Juvenile Ovine Hearts 2. Author Information Principal Investigator Contact Information Name: Frank Sachse Institution: University of Utah Address: The University of Utah, 95 S 2000 E Nora Eccles Harrison Salt Lake City, UT 84112 Email: frank.sachse@utah.edu Alternate Contact Information Name: Brian Cottle Institution: University of Utah Address: The University of Utah, 95 S 2000 E Nora Eccles Harrison Salt Lake City, UT 84112 Email: brian.cottle@utah.edu 3. Date of data collection: 20180101 - 20181201 4. Geographic location of data collection: Salt Lake City, UT 5. Information about funding sources that supported the collection of the data: This work was supported by the National Heart, Lung and Blood Institute (R56 HL128813 and R01 HL135077). We are grateful to Dr. Kurt H. Albertine (Internal Medicine, University of Utah, UT) for ovine heart specimens. We thank for discussions and feedback by Dr. Dylan Miller (Pathology, Intermountain Healthcare) and Dr. Monica P. Revelo (Pathology, University of Utah, UT). -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: Creative Commons License - CC BY NC Allows others to use and share your data non-commercially and with attribution 2. Links to publications that cite or use the data: Johnson JK, Cottle BK, Mondal A, Hitchcock R, Kaza AK, Sachse FB (2020) Localization of the sinoatrial and atrioventricular nodal region in neonatal and juvenile ovine hearts. PLoS ONE 15(5): e0232618. https://doi.org/10.1371/journal.pone.0232618 3. Links to other publicly accessible locations of the data: N/A 4. Links/relationships to ancillary data sets: N/A 5. Was data derived from another source? N/A 6. Recommended citation for the data: Sachse, Frank, Cottle, Brian and Jordan Johnson. 2019. Data for: Localization of the Sinoatrial and Atrioventricular Nodal Region in Neonatal and Juvenile Ovine Hearts. The Hive: University of Utah Research Data Repository. --------------------- DATA & FILE OVERVIEW --------------------- 1. Naming convention: This dataset contains more than 400 jpg slide scans of Masson's trichrome stains of nodal tissue from ovine hearts. The hearts are identified using the following labels: A1, A3, 646, 522, 300, 173, 172, and Donor. There is one heart from which only an AVN region was harvested, identified as 616. The images are organized according to heart and node in that heart. For each heart only one piece of AVN tissue was processed. For each heart from which the SAN region was processed at least one piece of tissue was processed, and in most cases two separate pieces of heart tissue were processed. Each AVN slide scan is named according to the following naming convention: [Heart Identifier]_AVN_[slice number]A.jpg As an example, a slide scan of the 23rd section of AVN tissue from the heart 300 would be named as follows: 300_AVN_23A.jpg Each SAN slide scan is named according to the following naming convention: [Heart Identifier]_SAN[1st or 2nd piece of SAN tissue]_[slice number]A.jpg As an example, a slide scan of the 5th section of SAN tissue from the second piece of the SAN region from the heart 646 would be named as follows: 646_SAN2_5A.jpg 2. Organization of files: In the dataset there are 17 .zip files. Each of the .zip files follows this naming convention: [Heart Identifier]_[Node (SAN or AVN)].zip For example, the SAN images of the heart 172 would all be contained within the .zip file: 172_SAN.zip -------------------------- METHODOLOGICAL INFORMATION -------------------------- From each heart tissues were excised from each of the two nodal regions (sinoatrial (SAN) and atrioventricular (AVN) nodes). The AV included the two nodal extensions, the compact nodal body, and the bundle of his. Excised AVN regions spanned from proximal to the coronary sinus ostium to the membranous septum, and cephalic to the tendon of Todaro to below the annulus of the tricuspid valve septal leaflet. The entire triangle of Koch and cephalic portions of the left and right bundle branches were included in the AVN regions. The post menstrual ages in months of the sheep from which these hearts were obtained at time of sacrifice are as follows: A1 = 4.4 A3 = 4.928 646 = 5.77 522 = 7.2 300 = 10.9 173 = 11.8 172 = 12 Donor = 58.3 Excised tissue samples were marked for identification of the sectioning face with a tissue dye that withstood paraffinization (CDI's Tissue Marking Dyes, Cancer Diagnostics, Inc.). Samples were then dehydrated through a gradient of ethanol and deionized water solutions which ended in 100% ethanol. After dehydration, the tissue was cleared with a gradient of paraffin-miscible organic solvent called Citrisolv and ethanol solutions. Clearing ended with immersion in 100% Citrisolv. The tissue was then immersed in paraffin solutions with decreasing amounts of Citrisolv and placed in a heated vacuum container at 60 C. Tissue was completely infiltrated by paraffin wax after two immersion steps in 100% paraffin. Times for each step varied based on tissue sample size. Paraffinized tissue was then placed in a paraffin mold and oriented so that the marked sectioning face of the tissue was accessible. Paraffin blocks hardened overnight. Sectioning was performed on a HistoCore BIOCUT microtome (Leica Biosystems, Wetzlar, Germany). Paraffin blocks were immersed in a solution of ice water and 16.67% cationic softening agents by volume to minimize section tearing. 8-10 serial sections with a thickness of 4 m were collected every 100 m throughout each tissue sample. AVN samples were sectioned from CS to MS. SAN samples were sectioned from RA-SVC junction to RA-IVC junction along the crista terminalis. Sections were collected on positively charged tissue adhesion slides and placed on a slide warmer until paraffinized sections were flush across the slide. Completed slides were stored at room temperature. SAN and AVN samples from one ovine heart were also sectioned parallel to the epicardial and endocardial tissue surface, respectively. Half of the collected sections were stained using an automated Masson's trichrome protocol on an automated staining device (Dako Corporation, Carpinteria, CA). Stain immersion duration and differentiation were verified using liver tissue sections of the same thickness every 16 sections. Imaging of the serial sections was performed on an AXIOSCAN Z.1 slide scanner (Cark Zeiss AG, Oberkochen, Germany) using a 40x objective as well as automated section identification and focus protocols. Image screening, pre-processing, including color balance adjustment and rotation, were performed using Fiji. For subsequent analyses, only images of tissue sections without tearing and folding artifacts were added to the dataset. Note that each slide scan has a number that indicates what its position is in the order of slices, and that for the most part every other image was included. This means that, though slices were taken every 100m, most slices are 200m apart. This is because slices were taken every 10m, but only every other slice was stained using a Masson's trichrome. 7. People involved with sample collection, processing, analysis and/or submission: Jordan Johnson, Brian Cottle, Frank Sachse