Select the download icon() to download data from any of the datasets below. For some data types multiple options may be available. For these types, a window displays that allows you to choose specific files.
UCSC Track Hubs
REST API / R
RNA-Seq
DNA-Seq
Microarray
Genomic Marker
Publications
PhenoGen UCSC Genome Browser Track Hubs
In addition to making the tracks available in our browser most tracks are available in a format to use with
the UCSC Genome
Browser. Please click on
any link below to visit the UCSC Genome Browser with PhenoGen tracks. Tracks below are added as a track hub
with multiple tracks you
can adjust through the genome browser.
Track hubs should remain linked to your UCSC rn7 genome view until you disconnect the track hub.
Note: Many tracks may not be displayed by default as strain specific read counts in a tissue may have more than 100 tracks. If you are unfamiliar with the UCSC Genome browser you can select tracks to display below the image.
Note: Many tracks may not be displayed by default as strain specific read counts in a tissue may have more than 100 tracks. If you are unfamiliar with the UCSC Genome browser you can select tracks to display below the image.
HRDP v7 - rn7 - Feb 2024
Transcriptomes with Merged Tissue Specific Read Counts:
MultiTissue
Transcriptome
Whole Brain Transcriptome
Liver Transcriptome
Kidney Transcriptome
Heart Transcriptome
Whole Brain Transcriptome
Liver Transcriptome
Kidney Transcriptome
Heart Transcriptome
Strain/Tissue Specific Read Counts (Sampled):
Randomly sampled to even total counts between strains to match the lowest strain.
Available Soon
Strain/Tissue Specific Read Counts (Total):
Not sampled: Each strain contains the total reads from all 3 biological replicates.
Available Soon
HRDP v6 - rn7 - Sept 2022
Transcriptomes with Merged Tissue Specific Read Counts:
MultiTissue
Transcriptome
Whole Brain Transcriptome
Liver Transcriptome
Kidney Transcriptome
Heart Transcriptome
Whole Brain Transcriptome
Liver Transcriptome
Kidney Transcriptome
Heart Transcriptome
Strain/Tissue Specific Read Counts (Sampled):
Randomly sampled to even total counts between strains to match the lowest strain.
Whole
Brain Strain Specific Reads Counts (Sampled)
Liver Strain Specific Reads Counts (Sampled)
Heart Strain Specific Reads Counts (Sampled)
Kidney Strain Specific Reads Counts (Sampled)
Liver Strain Specific Reads Counts (Sampled)
Heart Strain Specific Reads Counts (Sampled)
Kidney Strain Specific Reads Counts (Sampled)
Strain/Tissue Specific Read Counts (Total):
Not sampled: Each strain contains the total reads from all 3 biological replicates.
PhenoGen REST API
We are building a REST API to provide access to all public data. Eventually this will also
include running most functions available through the website. Keep checking back for new functions.
Domains for Functions Calls:
Functions can be called at either:
https://rest.phenogen.org
or
https://rest-test.phenogen.org
Please note this is a development and testing version of the API. Please do not use this for actual data analysis. Only for development.
https://rest.phenogen.org
or
https://rest-test.phenogen.org
Please note this is a development and testing version of the API. Please do not use this for actual data analysis. Only for development.
Help
Documentation at https://rest-doc.phenogen.org
All functions should include help as a response if you call the function with this appended to the end `?help=Y`. The response returns a JSON object with supported methods and then list of parameters and description of each parameter as well as a list of options if there is a defined list of values.
PhenoGenRESTR
An R package that we're maintaining as new REST API Functions are developed to download data directly into R.
R Package Documentation
*The mask files are the same for all of these datasets.
New RNA Sequencing Datasets Experimental Details/Downloads