Dataset DOI: 10.5061/dryad.fttdz096z

Description of the data and file structure

Excel files of raw data for physiology and histology assessments in adult male C57/Bl6J mice treated with PCBs for 2 months.

Files and variables

File: adult_male_vsa_data.xlsx

Description: Raw data generated from running void spot assays (VSA) on adult wild-type male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. For VSA mice are placed on a filter paper for 4 hours and then the filter papers containing urine spots were imaged with UV light. The resulting images were analyzed via Void Whizzard software freely available as a plugin in Image J. This Excel table is the readout of the Void Whizzard analysis of the urine content on the assay papers. Each column is the voiding parameter examined, and each row is a different animal.

Variables

• The first tab of the excel sheet is the Void Whizzard data analysis. The first column (A) is the animal's unique ID, the second column (B) is the treatment group of that animal, column C is the total urine spot count, column D is the total urine area on the paper in cm2, column E is the percent of the urine area in the center of the paper, column F is the percent of the urine area in the corners of the paper. Columns G-N are the number of urine spots that fall into a specific size bin labeled from (0-0.1cm2) to  (4+cm2) . Each column is the voiding parameter examined, and each row is a different animal.
• The second tab of the excel sheet labeled frequent spotter refers to the number of animals that fall into the listed categories in column A. The number of animals from each of the treatment groups indicated in column B-E (B=control, C=0.1mg/kgPCB, D=1mg/kgPCB, E=6mg/kgPCB group) that had more than 50+ spots, 100+ spots, 200+spots, 300+ spots, 400+spots.

File: Adult_Male_Uroflow_Analysis.xlsx

Description: Raw data generated from running uroflowmetry on adult wild-type male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. After the assay, the videos captured by Raspberry Pi units during uroflowmetry testing were analyzed. This Excel table is the analysis of each captured void. Each column header is a parameter examined, and each row is a void event for each different animal. Columns V through AC are the averages of all parameters from all voids from a single animal.

Variables

• Each row is a void event for each different animal. The first column (A) is the animal's unique ID, and the second column (B) is the treatment of that animal. Column C is the total number of void events for that animal. Column D is the number of urine events that can be used to capture a mass and time, as they did not hit the sides of the chamber or the bars and thus are voids that can be used for an accurate flow rate. Column E is the time on the file of the void event. Column F is the time stamp on the scale prior to a change in mass right before the void. Column G is the time stamp at the time that the scale mass stops increasing after the void. Column H is the mass of the scale right before the void, column I is the final mass after the void. Column J is the calculated final-initial change in mass of the void. Column K is this converted to volume. Column L and M are just the seconds portion captured from the time stamp to more easily calculate the time change of the void which is in column N. Column O is the flow rate (volume/time). Column P is the blinded viewers assessment of the stream, a strong stream =3 a drop stream =0. Each void if it was not obscured by the bars of the floor grid gets a stream rating. Column Q is the time between void events. Colum R is the mouse ID. Column S is the number of fecal events during the testing.  Columns T through AA are the averages of all previous layed out parameters from all voids from a single animal.

File: adult_male_cmg_analysis.xlsx

Description: Raw data generated from running anesthetized cystometry on wild-type animals treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. Labchart software was used to assess the time and pressure for each voiding parameter assessed including baseline pressure, threshold pressure, peak pressure. This Excel table is the analysis of each of 5 consecutive voids for each animal each in its own tab. The highlighted cells in each tab are the template areas where the values from the cystometrogram are added in for each void if that parameter was examined in this study. The last tab of the excel sheet contains the 5 void average summary for each animal whose ID is identified in Row 3 for each void parameter (Row 4-10) for each experimental treatment group.

Variables

• This Excel table is the analysis of each of 5 consecutive voids for each animal each in its own tab.  For each individual tab which is one animal, this is a template with columns G-Z spanning 5 individual void events analyzed. The template has measures to add in by the user for ease of interpretation. The previous peak (row 6), baseline pressure, threshold pressure and maximum pressure (rows 8-10 respectively) are copied and pasted for that void from the LabChart trace of the pressure volume cystometrogram tracing. The number of non void contractions (row 13) is entered by the blinded investigator. The value in the stop position on row 4 for void #5 is also pasted in from the LabChart software for the stop of the last void. The remaining variables described in the rows are calculated automatically or are not used in this data. The template remains for ease of use and consistency even if not all parameters are assessed in a certain type of assay. Column A lines 26-37 will automatically average the 5 void parameters entered as above. These values are then copied into the last tab which contains the 5 void average summary for each individual animal ID identified in Row 3 for each void parameter (Row 4-10).

File: Adult_Male_Ki67_.xlsx

Description: Raw data generated from quantifying the percentage of Ki67 positive cells from images of prostate tissues from wild-type adult male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. Each column header is an endpoint examined, and each row is a different image, separated out for each animal and prostate lobe.

Variables

• All column headers describe the protein marker expressed, the cell count, or average; each row is an image, which is separated out for each animal and prostate lobe. Column A is the blinded name give to the image group during blinded analysis, Column B is the prostate lobe examined, Column C is the PCB dose group, Column D is the animal number within that group, Column E is the image number for that given animal. For example 3 images (Column E) may be taken from a single animal (Column D). Column F is the blinded count for the number of Ki67 positive cells in the epithelium for that image. Column G  is the count for the stroma. Column H is the sum of column F and G for a total. Column I-K is the total number of epithelial cells, stromal cells and total cell counts respectively. Colum L is for comments, Column M-O are the raw Ki67 counts divided by total cells in the epithelium, stroma and total respectively as a percent. Column P-R are the averages across images from the same animal. Column S-U are the averages across an animal which is the values used for statistical comparisons.

File: Adult_Male_Caspase_Counts.xlsx

Description: Raw data generated from quantifying the percentage of Caspase 3 positive cells from images of prostate tissues from wild-type adult male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. Each column header is an endpoint examined, and each row is a different image, separated out for each animal and prostate lobe.

Variables

• All column headers describe the protein marker expressed, the cell count, or average; each row is an image, which is separated out for each animal and prostate lobe. Tab one is the data for anterior and ventral prostate, tab 2 is the data for dorsal prostate. In Tab one Column A is the image group ID, Column B is the animal ID, Column C is the image number for that animal, Column D is the prostate lobe, Column E is the dose group, Column F is the number of blinded counted Caspase 3 positive cells in the epithelium. Column G is the number of blinded counted Caspase 3 positive cells in the stroma and Column H is the total of these two. Columns I-K are the total number of epithelial, stromal and total cells respectively for any images which had a positive caspase cell in it. Column L-N are the percent of caspase 3 positive cells over total cells for the epithelium, stroma and total respectively. Columns O-Q are the average per image from the same animal, Columns R-T are the averages across an animal which are the values used for statistical comparisons.

File: Adult_Male_Smooth_Muscle_Count.xlsx

Description: Raw data generated from quantifying the thickness of smooth muscle (stained with Acta2) from images of prostate tissues from wild-type adult male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. Each column header is an endpoint examined, and each row is a different image, separated out for each animal and prostate lobe.

Variables

• All column headers describe the endpoint, the measure, or average; each row is an image, which is separated out for each animal and prostate lobe. There is a tab for each prostate lobe. Column A-E are the file name, dose group, animal number, image number and prostate lobe examined. Column F is the average thickness of the muscle from several regions within each image within each section. Colun G is the average thickness per image. Column H is the conversion to mm from pixels. Column I is the average thickness per animal. Column J is the average thickness with animal replicates averaged which are the values used for statistical comparisons.

File: Ki67.zip

Description: The raw fluorescent images of the prostate lobe slides incubated with antibodies targeting Ki67 (green) and e-cadherin (red) and counterstained with DAPI (blue) to label nuclei. The main Ki67 folder once open is then split into 3 folders one each for each prostate lobe examined (Anterior, Dorsal and Ventral) each of these folders contains a folder for slide set 1 and slide set 2 of images. Each of the slide set 1 and 2 folders contains a folder for each of the dose groups of control, 0.1mg/kg, 1mg/kg and 6mg/kg PCB groups.

File: caspase_3.zip

Description: The raw fluorescent images of the prostate lobe slides incubated with antibodies targeting caspase 3 (red) and e-cadherin (green) and counterstained with DAPI (blue) to label nuclei. The main Caspase folder once open is then split into 3 folders one each for each prostate lobe examined (Anterior, Dorsal and Ventral) each of these folders contains a folder for slide set 1 and slide set 2 of images. Each of the slide set 1 and 2 folders contains a folder for each of the dose groups of control, 0.1mg/kg, 1mg/kg and 6mg/kg PCB groups.

File: Adult_Male_Study.xlsx

Description: Excel file containing the animal IDs, and body mass and prostate, testes and seminal vesicle mass metrics at time of collection from wild-type adult male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. Each row is a different animal. Column headers describe the parameter.

Variables

• Excel file containing Column A, the animal IDs, Column B the sex, Column C the dose group, Column D the body mass, Column E-H prostate mass for each lobe listed, Column I-L are the prostate masses normalized to body mass for each lobe respectively. Column M and N are the testes mass and testes mass normalized to body mass. Columns 0-P are seminal vesicle mass alone and normalized to body mass at time of collection. A blank means that parameter was not collected for that animal. Each row is a different animal. Column headers describe the parameter.

File: VSA_images.zip

Description: Images of papers from void spot assay (VSA) imaged under UV light from wild-type adult male mice treated with vehicle or 0.1, 1 or 6mg/kg/d PCBs for 2 months. All file names are the animal ID which can be found in the excel sheet for VSA.  All images in this folder are Tiffs of the imaged paper that was placed in the cage for the mouse to urinate on for 4 hours.

File: smooth_muscle.zip

Description: The raw fluorescent images of the prostate lobe slides incubated with antibodies targeting Acta2 (green) and e-cadherin (red) and counterstained with DAPI (blue) to label nuclei. The main folder once open is then split into 3 folders one each for each prostate lobe examined (Anterior, Dorsal and Ventral) each of these folders contains a folder for slide set 1 and slide set 2 of images. Each of the slide set 1 and 2 folders contains a folder for each of the dose groups of control, 0.1mg/kg, 1mg/kg and 6mg/kg PCB groups.

Code/software

Excel

Image J

Any photo viewer