Targeted RNA-sequencing of aged FFPE liver tissue data
Gene expression data on >20 year-old, paired frozen and archival FFPE liver samples generated using targeted resequencing (TempO-Seq) and whole-genome RNA-sequencing methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313 and 427 mg/kg-day, (n=6/dose) by drinking water for 6 days. Portions of this dataset are inaccessible because: Including all of these files on ScienceHub would exceed the 1 Gb limit. They can be accessed through the following means: The data is stored on the L: Drive. Information on all of the files and file paths are indicated in the 20210923_Readme.xlsx file uploaded with the data. Format: Excel files, tab delimited files, csv files, and sequencing FASTQ files.
This dataset is associated with the following publication:
Cannizzo, M., C. Wood, S. Hester, and L. Wehmas. Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicology Reports. Elsevier B.V., Amsterdam, NETHERLANDS, 9: 883-894, (2022).
Resources
4 resources available
-
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78962
FILE -
20210908_DCA9402_Additional_Data.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
20210908_DCA9402_MS_tables.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET -
20210923_Readme.xlsx
APPLICATION/VND.OPENXMLFORMATS-OFFICEDOCUMENT.SPREADSHEETML.SHEET
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "020:00" ] |
| contactPoint |
{ "fn": "Leah Wehmas", "hasEmail": "mailto:wehmas.leah@epa.gov" } |
| description | Gene expression data on >20 year-old, paired frozen and archival FFPE liver samples generated using targeted resequencing (TempO-Seq) and whole-genome RNA-sequencing methods. Samples were originally collected from male mice exposed to a reference chemical (dichloroacetic acid, DCA) at 0, 198, 313 and 427 mg/kg-day, (n=6/dose) by drinking water for 6 days. Portions of this dataset are inaccessible because: Including all of these files on ScienceHub would exceed the 1 Gb limit. They can be accessed through the following means: The data is stored on the L: Drive. Information on all of the files and file paths are indicated in the 20210923_Readme.xlsx file uploaded with the data. Format: Excel files, tab delimited files, csv files, and sequencing FASTQ files. This dataset is associated with the following publication: Cannizzo, M., C. Wood, S. Hester, and L. Wehmas. Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicology Reports. Elsevier B.V., Amsterdam, NETHERLANDS, 9: 883-894, (2022). |
| distribution |
[ { "title": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78962", "accessURL": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78962" }, { "title": "20210908_DCA9402_Additional_Data.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1523143/20210908_DCA9402_Additional_Data.xlsx" }, { "title": "20210908_DCA9402_MS_tables.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1523143/20210908_DCA9402_MS_tables.xlsx" }, { "title": "20210923_Readme.xlsx", "mediaType": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", "downloadURL": "https://pasteur.epa.gov/uploads/10.23719/1523143/20210923_Readme.xlsx" } ] |
| identifier | https://doi.org/10.23719/1523143 |
| keyword |
[ "Formalin-fixed paraffin-embedded (FFPE)", "RNA-sequencing", "benchmark dose analysis", "dichloroacetic acid" ] |
| license | https://pasteur.epa.gov/license/sciencehub-license.html |
| modified | 2021-09-23 |
| programCode |
[ "020:000" ] |
| publisher |
{ "name": "U.S. EPA Office of Research and Development (ORD)", "subOrganizationOf": { "name": "U.S. Environmental Protection Agency", "subOrganizationOf": { "name": "U.S. Government" } } } |
| references |
[ "https://doi.org/10.1212/nxi.0000000000001078" ] |
| rights |
null
|
| title | Targeted RNA-sequencing of aged FFPE liver tissue data |
