Data Package Metadata View Summary

Flow cytometry data: female mice exposed for 60 days to uranium in drinking water 040518 – bone marrow erythroid cells

General Information

Data Package:
Local Identifier:	edi.352.1
Title:	Flow cytometry data: female mice exposed for 60 days to uranium in drinking water 040518 – bone marrow erythroid cells
Alternate Identifier:	DOI PLACE HOLDER
Abstract:	A total of 21 female, 6 week old C57BL/6J mice were exposed via drinking water to 0, 5 and 50 ppm uranium (in the form of uranyl acetate; UA) for 60 days (7 mice per group). Mice were 15 week old at the end of exposures. This experiment was performed to examine the effects of 60 day in vivo uranium exposure on 1) the immune function of splenocytes 2) spleen lymphocyte population subsets 3) thymus lymphocyte population subsets; 4) bone marrow erythroid cells; 5) Uranium concentrations in kidney, femur bone, liver, blood, spleen, thymus and bone marrow Conclusions: No differences between treatments; data not associated with publication.
Publication Date:	2020-03-11

Time Period

Begin:

2018-04-05

End:

2018-06-04

People and Organizations
Contact:	Lauer, Fredine T (Department of Pharmaceutical Sciences University of New Mexico) [ email ]
Creator:	Lauer, Fredine T (Department of Pharmaceutical Sciences University of New Mexico)
Associate:	Bolt, Alicia (Department of Pharmaceutical Sciences University of New Mexico, Investigator)
Associate:	Medina, Sebastian (Department of Pharmaceutical Sciences University of New Mexico, Investigator)
Associate:	Burchiel, Scott (Department of Pharmaceutical Sciences University of New Mexico, Principal Investigator)

Data Entities
Data Table Name:	FCS Manifest
Description:	Manifest of flow cytometry (.fcs) files included in this data package
Data Table Name:	Fluorescence reagent table
Description:	Each sample has been stained according to the fluorescence reagent table
Data Table Name:	Reagent descriptions
Description:	Detailed descriptions of reagents used
Data Table Name:	Compensation matrix
Description:	Fluorescent compensations used to distinguish relative spectral contribution from sensors
Data Table Name:	Gating strategy
Description:	Description of gating strategy used to distinguish cellular subpopulations
Other Name:	FCS files
Description:	Compressed directory of FCS files
Other Name:	Gating strategy diagram
Description:	Image of gating strategy

Detailed Metadata

Data Entities

Data Table


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Name:	FCS Manifest
Description:	Manifest of flow cytometry (.fcs) files included in this data package
Number of Records:	24
Number of Columns:	3

Table Structure

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Table Column Descriptions

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FCSfileName

animalID

doseGroup

Definition:

Name of .fcs file

Unique ID of animal observed in .fcs file

Uranium concentration dosage group

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Definition

Uranium concentration dosage group

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Data Table


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Optical detector

Reporter

Sample

Definition:

An optical detector is a part of a flow cytometry instrument that serves as a sensor of light or other electromagnetic energy that is being converted to electrical signal. Typically, photodiodes and photomultiplier tubes are used as optical detectors in flow cytometry.

A component of a fluorescence reagent plays the role of an analyte reporter if it reports the presents of the analyte. Typically, an analyte detector has fluorescence characteristics that are detectable by a flow cytometry instrument and thus useful for reporting analytes.

Sample identifier

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Analyte

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Reporter

Manufacturer

Clone

Catalog No.

Definition:

Relative amount of molecules properties or processes being evaluated

Material (e.g., a substance or chemical constituent) plays the role of analyte in an experiment if it is the subject of interest of an analytical procedure within the experiment (i.e., it is being quantified in the experiment).

A component of a fluorescence reagent plays the role of an analyte detector if it makes the analyte detectable. Typically, the analyte detector chemically binds to an analyte and thus can be used to detect the analyte.

Manufacturer of reagent

If the probe is a monoclonal antibody the clone name or number

Reagent catalog number

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Relative amount of molecules properties or processes being evaluated

Definition

Manufacturer of reagent

Definition

If the probe is a monoclonal antibody the clone name or number

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Methods:

Data Table


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Name:	Compensation matrix
Description:	Fluorescent compensations used to distinguish relative spectral contribution from sensors
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Table Structure

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Table Column Descriptions

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FL1

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Definition:

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Accuracy Assessment:

Coverage:

Methods:

Data Table


Data:	https://pasta-s.lternet.edu/package/data/eml/edi/352/1/bd6f2b6ee7ddab9e9556360dcbbab9a5
Name:	Gating strategy
Description:	Description of gating strategy used to distinguish cellular subpopulations
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Table Structure

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Gate description

Image

Definition:

Unique identifer of cellular subpopulation

Description of subpopulation identified by gate

Image file showing gating strategy

Storage Type:

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Measurement Type:

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Definition

Gate ID

Definition

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Definition

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Accuracy Assessment:

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Methods:

Non-Categorized Data Resource

Name:

FCS files

Entity Type:

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Description:

Compressed directory of FCS files

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Gating strategy diagram

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Image of gating strategy

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Data:

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Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data (Data User herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available as is. The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)	Uranium, drinking water exposure, immunotoxicity, humoral immunity, innate immunity

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package

Description:

Experiment variables: C57BL/6J female mice; uranium in drinking water for 60day at 0, 5 and 50 ppm. Mice were housed 4 to a cage and 3 to a cage (7 mice total) per exposure.

Description:

Sample characteristics: BM cells at 1x10^6 cell/ml were stained with 0.5 µg Ab. Ter119 and CD71

Treatment: bone marrow cells from 60d uranium treated female mice:

1) 1x10^6 cell/ml/tube were washed 1x with wash/stain buffer (DPBS without Ca or Mg + 2%FBS + 0.09% sodium azide). Centrifugation was ran for 10 min at 228 xg. Wash solution was aspirated.

2) 100 µl of antibody cocktail (antibody concentration = 5 µg/ml) was added to the appropriate sample tubes. Unstained control sample contained 100 µl wash/stain buffer (no antibody). Single stain controls contained 100µl of wash/stain buffer + the antibody to yield a 5µg/ml concentration (see fluorescence reagents description).

3) Vortexed gently and incubated at 4˚C for 30 min in the dark.

4) Added 2 ml of wash/stain buffer, centrifuged, aspirate.

5) Resuspended cells in 0.5 ml wash/stain buffer.

6) Covered tubes with aluminum foil to protect from the light and analyzed on an AccuriC6 Flow Cytometer.

Description:

INSTRUMENT CONFIGURATION AND SETTINGS:

Flow cell and fluidics: The instrument has not been altered; fixed-alignment 200µm ID quartz capillary

Light source(s): Blue laser was replaced 03/30/2016 by BDBiosciences; 488 nm Solid State Blue Laser 20 mW; 640 nm Diode Red Laser 14.7 mW

Excitation optics configuration: The instrument has not been altered. 488nm and 640nm

Optical filters: The instrument has not been altered, all filters are original and came with the instrument. FL1 533/30nm (e.g. FITC/GFP) FL2 585/40nm (e.g. PE/PI) FL3 >670nm (e.g. PerCP, PerCP-Cy5.5, PE-CY7) FL4 675/25nm (e.g. APC)

Optical detectors: FL1 FITC Ter119; FL2 PE CD71

Instrument(s):

Instrument manufacturer: BD Biosciences http://www.bdbiosciences.com/home/ Instrument model: Accuri C6

Sampling Area and Study Extent

Sampling Description:

Age: Mice were purchased at 6 weeks of age; Mice were 15 weeks old at end of experiment.

Bone marrow cells isolated from bone marrow of 2 femurs of mice exposed to uranium in the drinking water at 0, 5 and 50 ppm for 60 days. Bone marrow cells were isolated from femurs and resuspended at 1x106 cell/ml. One ml of cells from each sample was aliquoted into one, 12x75 mm FACS tube for staining. Antibodies included Ter-119 and CD71.

Bone marrow from 2 femurs (per mouse) exposed to uranium in drinking water. N=7 mice per group

Sampling Extent:

Taxonomic Range:

General Coverage:

Mus musculus. C57BL/6J; Jackson Laboratory, Sacramento, CA

Classification:

Common Name:

female mice

Quality Control
Quality Control Step 1:

Description:

Mice exposed to 0 ppm were control group. Unstained as well as single stain controls were used as appropriate. Bone marrow cells collected from both femurs for phenotyping; single stains (PE and FITC) and were used for color compensation.

People and Organizations

Creators:

Individual:

Fredine T Lauer

Organization:

Department of Pharmaceutical Sciences University of New Mexico

Email Address:

FLauer@salud.unm.edu

Contacts:

Individual:

Fredine T Lauer

Organization:

Department of Pharmaceutical Sciences University of New Mexico

Email Address:

FLauer@salud.unm.edu

Associated Parties:

Individual:

Alicia Bolt

Organization:

Department of Pharmaceutical Sciences University of New Mexico

Email Address:

ambolt@salud.unm.edu

Role:

Investigator

Individual:	Sebastian Medina
Organization:	Department of Pharmaceutical Sciences University of New Mexico
Role:	Investigator

Individual:	Scott Burchiel
Organization:	Department of Pharmaceutical Sciences University of New Mexico
Role:	Principal Investigator

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period

Begin:

2018-04-05

End:

2018-06-04

Taxonomic Range:

General Coverage:

Mus musculus. C57BL/6J; Jackson Laboratory, Sacramento, CA

Classification:

Common Name:

female mice

Project

Parent Project Information:

Title:

Metals Exposure and Toxicity Assessment on Tribal Lands in the Southwest (METALS)

Personnel:

Individual:	Scott Burchiel
Organization:	Department of Pharmaceutical Sciences University of New Mexico
Role:	Principal Investigator

Funding:

USEPA: 1P42ES025589

Maintenance

Maintenance:

Description:	completed
Frequency:

Other Metadata

Copyright 2024 Environmental Data Initiative. This material is based upon work supported by the National Science Foundation under grants #2223103 and #2223104. Any opinions, findings, conclusions, or recommendations expressed in the material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. Please contact us with questions, comments, or for technical assistance regarding this web site or the Environmental Data Initiative. Please read our privacy policy to know what information we collect about you and to understand your privacy rights.

EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

Data Package Metadata View Summary

Flow cytometry data: female mice exposed for 60 days to uranium in drinking water 040518 – bone marrow erythroid cells

Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

Data Package Usage Rights

Keywords

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Parent Project Information:

Maintenance

Recently Added

Recently Updated

Data Package Metadata View Summary

Flow cytometry data: female mice exposed for 60 days to uranium in drinking water 040518 – bone marrow erythroid cells

+/- Data Entities

Data Table

Data Table

Data Table

Data Table

Data Table

Non-Categorized Data Resource

Non-Categorized Data Resource

+/- Data Package Usage Rights

+/- Keywords

+/- Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

+/- People and Organizations

+/- Temporal, Geographic and Taxonomic Coverage

+/- Project

Parent Project Information:

+/- Maintenance

Data Entities

Data Package Usage Rights

Keywords

Methods and Protocols

People and Organizations

Temporal, Geographic and Taxonomic Coverage

Project

Maintenance