Select the download icon(
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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 v7.1 - rn7 - Aug 2024
IsoSeq Alignments:
Brain/Liver High Quality IsoSeq Alignment Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| Whole Brain IsoSeq | High Quality IsoSeq Concensus Sequences aligned to the HRDPv7 genomes. Following alignment 4 strains were merged into a single alignment(BAM) deduplicated transcripts with exactly matching introns and within 10bp at 5' end and 30bp at 3' end, assigned transcript IDs by matching across tissues, and then assigned to genes by matching isoforms with a shared exact match for a splice junction or overlapping single exons. |
| Liver IsoSeq | High Quality IsoSeq Concensus Sequences aligned to the HRDPv7 genomes. Following alignment 4 strains were merged into a single alignment(BAM) deduplicated transcripts with exactly matching introns and within 10bp at 5' end and 30bp at 3' end, assigned transcript IDs by matching across tissues, and then assigned to genes by matching isoforms with a shared exact match for a splice junction or overlapping single exons. |
| Merged IsoSeq | Complete transcriptome of unique IsoSeq transcripts from Whole Brain and Liver as matched between tissues. |
RNA-Seq Reconstructed Transcriptomes with Merged Tissue Specific Read Counts:
Female Whole Brain/Liver Transcriptome Track Hub - Show Individual Tracks
MultiTissue Transcriptome Track Hub - Show Individual Tracks
Whole Brain Transcriptome Track Hub - Show Individual Tracks
Liver Transcriptome Track Hub - Show Individual Tracks
Kidney Transcriptome Track Hub - Show Individual Tracks
Heart Transcriptome Track Hub - Show Individual Tracks
| Whole Brain | Liver | ||
|---|---|---|---|
| Track Name (UCSC Track Link) | Description | Track Name (UCSC Track Link) | Description |
| PhenoGen Whole Brain HRDPv7 Transcriptome | Whole brain ribosome depleted totalRNA transcriptome reconstruction. (73 strains) v7.1 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. | PhenoGen Liver HRDPv7 Transcriptome (HRDPv7) | Liver ribosome depleted totalRNA transcriptome reconstruction. (62 strains) v7.1 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Splice junctions Merged BNLx/SHR | Splice junctions from the merged BNLx/SHR samples at PreE,E,PostE time points generated by regtools - v1.0.0. | Splice junctions Merged BNLx/SHR | Splice junctions from the merged BNLx/SHR samples at PreE,E,PostE time points generated by regtools - v1.0.0. |
| Splice junctions Pre-Estrous BNLx/SHR | Splice junctions from the merged Pre-Estrous BNLx/SHR samples generated by regtools - v1.0.0. | Splice junctions Pre-Estrous BNLx/SHR | Splice junctions from the merged Pre-Estrous BNLx/SHR samples generated by regtools - v1.0.0. |
| Splice junctions Estrous BNLx/SHR | Splice junctions from the merged Estrous BNLx/SHR samples generated by regtools - v1.0.0. | Splice junctions Estrous BNLx/SHR | Splice junctions from the merged Estrous BNLx/SHR samples generated by regtools - v1.0.0. |
| Splice junctions Post-Estrous BNLx/SHR | Splice junctions from the merged Post-Estrous BNLx/SHR samples generated by regtools - v1.0.0. | Splice junctions Post-Estrous BNLx/SHR | Splice junctions from the merged Post-Estrous BNLx/SHR samples generated by regtools - v1.0.0. |
| Whole Brain Female Merged(BNLx/SHR) totalRNA (HRDPv7) + strand - strand |
Whole brain ribosome depleted totalRNA read depth track includes female data at Pre-Estrous, Estrous, and Post-Estrous time points. | Liver Female Merged(BNLx/SHR) totalRNA (HRDPv7) + strand - strand |
Liver ribosome depleted totalRNA read depth track includes female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Whole Brain Female Merged(BNLx/SHR) totalRNA Estrous (HRDPv7) + strand - strand |
Whole brain ribosome depleted totalRNA read depth track includes female data at Estrous time points. | Liver Female Merged(BNLx/SHR) totalRNA Estrous (HRDPv7) + strand - strand |
Liver ribosome depleted totalRNA read depth track includes female data at Estrous time points. |
| Whole Brain Female Merged(BNLx/SHR) totalRNA Pre-Estrous (HRDPv7) + strand - strand |
Whole brain ribosome depleted totalRNA read depth track includes female data at Pre-Estrous time points. | Liver Female Merged(BNLx/SHR) totalRNA Pre-Estrous (HRDPv7) + strand - strand |
Liver ribosome depleted totalRNA read depth track includes female data at Pre-Estrous time points. |
| Whole Brain Female Merged(BNLx/SHR) totalRNA Post-Estrous (HRDPv7) + strand - strand |
Whole brain ribosome depleted totalRNA read depth track includes female data at Post-Estrous time points. | Liver Female Merged(BNLx/SHR) totalRNA Post-Estrous (HRDPv7) + strand - strand |
Liver ribosome depleted totalRNA read depth track includes female data at Post-Estrous time points. |
MultiTissue Transcriptome Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| PhenoGen Whole Brain HRDPv7 Transcriptome | Whole brain ribosome depleted totalRNA transcriptome reconstruction. (73 strains) v7 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Brain TotalRNA Plus 5 Billion Reads (HRDPv7) | Whole brain plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Brain TotalRNA Minus 5 Billion Reads (HRDPv7) | Whole brain minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| PhenoGen Liver HRDPv7 Transcriptome (HRDPv7) | Liver ribosome depleted totalRNA transcriptome reconstruction. (62 strains) v7 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Liver TotalRNA Plus 5 Billion Reads (HRDPv7) | Liver plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Liver TotalRNA Minus 5 Billion Reads (HRDPv7) | Liver minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| PhenoGen Heart HRDPv7 Transcriptome | Heart ribosome depleted totalRNA transcriptome reconstruction (21 strains) |
| Heart TotalRNA Plus Reads (HRDPv7) | Heart plus strand read depth using all of the samples merged together. |
| Heart TotalRNA Minus Reads (HRDPv7) | Heart minus strand read depth using all of the samples merged together. |
| PhenoGen Kidney HRDPv7 Transcriptome | Kidney ribosome depleted totalRNA transcriptome reconstruction. (28 strain) |
| Kidney TotalRNA Plus 5 Billion Reads (HRDPv7) | Liver plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Kidney TotalRNA Minus 5 Billion Reads (HRDPv7) | Liver minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| PhenoGen MultiTissue HRDPv7 Transcriptome (HRDPv7) | Merged across tissues/strains/sex ribosome depleted totalRNA transcriptome reconstruction (73 strains/Male and Female data). |
Whole Brain Transcriptome Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| PhenoGen Whole Brain HRDPv7 Transcriptome | Whole brain ribosome depleted totalRNA transcriptome reconstruction. (73 strains) v7 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Whole Brain TotalRNA Plus 5 Billion Reads (HRDPv7) | Whole brain plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Whole Brain TotalRNA Minus 5 Billion Reads (HRDPv7) | Whole brain minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Whole Brain TotalRNA Splice Junctions (HRDPv7) | Splice junctions generated by regtools - v1.0.0 from the merged 5 billion read sampled file. |
Liver Transcriptome Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| PhenoGen Liver HRDPv7 Transcriptome | Liver ribosome depleted totalRNA transcriptome reconstruction. (62 strains) v7 includes male data and female data at Pre-Estrous, Estrous, and Post-Estrous time points. |
| Liver TotalRNA Plus 5 Billion Reads (HRDPv7) | Liver plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Liver TotalRNA Minus 5 Billion Reads (HRDPv7) | Liver minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Liver TotalRNA Splice Junctions (HRDPv7) | Splice junctions generated by regtools - v1.0.0 from the merged 5 billion read sampled file. |
Kidney Transcriptome Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| PhenoGen Kidney HRDPv7 Transcriptome | Kidney ribosome depleted totalRNA transcriptome reconstruction. (28 strains) |
| Kidney TotalRNA Plus 5 Billion Reads (HRDPv7) | Kidney plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Kidney TotalRNA Minus 5 Billion Reads (HRDPv7) | Kidney minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Kidney TotalRNA Splice Junctions (HRDPv7) | Splice junctions generated by regtools - v1.0.0 from the merged 5 billion read sampled file. |
Heart Transcriptome Track Hub - Show Individual Tracks
| Track Name (UCSC Track Link) | Description |
|---|---|
| PhenoGen Heart HRDPv7 Transcriptome | Heart ribosome depleted totalRNA transcriptome reconstruction. (21 strains) |
| Heart TotalRNA Plus 5 Billion Reads (HRDPv7) | Heart plus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Heart TotalRNA Minus 5 Billion Reads (HRDPv7) | Heart minus strand read depth using 5 billion reads randomly sampled from all of the samples merged together. |
| Heart TotalRNA Splice Junctions (HRDPv7) | Splice junctions generated by regtools - v1.0.0 from the merged 5 billion read sampled file. |
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) -
Show Individual Tracks
Liver Strain Specific Reads Counts (Sampled) - Show Individual Tracks
Heart Strain Specific Reads Counts (Sampled) - Show Individual Tracks
Kidney Strain Specific Reads Counts (Sampled) - Show Individual Tracks
Liver Strain Specific Reads Counts (Sampled) - Show Individual Tracks
Heart Strain Specific Reads Counts (Sampled) - Show Individual Tracks
| HXB/BXH Strains | |||
|---|---|---|---|
| BN-Lx/Cub + strand - strand | BXH9/Cub + strand - strand | HXB3/Ipcv + strand - strand | HXB20/IpcvMcwi + strand - strand |
| SHR/OlaIpcv + strand - strand | BXH10/Cub + strand - strand | HXB5/Ipcv + strand - strand | HXB21/Ipcv + strand - strand |
| BXH2/CubMcwi + strand - strand | BXH11/Cub + strand - strand | HXB7/Ipcv + strand - strand | HXB24/Ipcv + strand - strand |
| BXH5/Cub + strand - strand | BXH12/Cub + strand - strand | HXB13/Ipcv + strand - strand | HXB25/Ipcv + strand - strand |
| BXH6/Cub + strand - strand | HXB1/Ipcv + strand - strand | HXB17/Ipcv + strand - strand | HXB29/Ipcv + strand - strand |
| BXH8/Cub + strand - strand | |||
Kidney Strain Specific Reads Counts (Sampled) - Show Individual Tracks
| HXB/BXH Strains | |||
|---|---|---|---|
| BN-Lx/Cub + strand - strand | BXH11/Cub + strand - strand | HXB7/Ipcv + strand - strand | HXB23/Ipcv + strand - strand |
| SHR/OlaIpcv + strand - strand | BXH12/Cub + strand - strand | HXB10/IpcvMcwi + strand - strand | HXB24/Ipcv + strand - strand |
| BXH2/CubMcwi + strand - strand | BXH13/Cub + strand - strand | HXB13/Ipcv + strand - strand | HXB25/Ipcv + strand - strand |
| BXH3/CubMcwi + strand - strand | HXB1/Ipcv + strand - strand | HXB15/Ipcv + strand - strand | HXB27/Ipcv + strand - strand |
| BXH6/Cub + strand - strand | HXB2/IpcvMcwi + strand - strand | HXB17/Ipcv + strand - strand | HXB29/Ipcv + strand - strand |
| BXH8/Cub + strand - strand | HXB3/Ipcv + strand - strand | HXB18/Ipcv + strand - strand | HXB31/IpcvMcwi + strand - strand |
| BXH9/Cub + strand - strand | HXB4/IpcvMcwi + strand - strand | HXB21/Ipcv + strand - strand | |
| BXH10/Cub + strand - strand | HXB5/Ipcv + strand - strand | HXB22/Ipcv + strand - strand | |
Strain/Tissue Specific Read Counts (Total):
Not sampled: Each strain contains the total reads from all 3 biological replicates.
Whole Brain Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
Liver Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
Heart Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
Kidney Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
Liver Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
Heart Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
| HXB/BXH Strains | |||
|---|---|---|---|
| BN-Lx/Cub + strand - strand | BXH9/Cub + strand - strand | HXB3/Ipcv + strand - strand | HXB20/IpcvMcwi + strand - strand |
| SHR/OlaIpcv + strand - strand | BXH10/Cub + strand - strand | HXB5/Ipcv + strand - strand | HXB21/Ipcv + strand - strand |
| BXH2/CubMcwi + strand - strand | BXH11/Cub + strand - strand | HXB7/Ipcv + strand - strand | HXB24/Ipcv + strand - strand |
| BXH5/Cub + strand - strand | BXH12/Cub + strand - strand | HXB13/Ipcv + strand - strand | HXB25/Ipcv + strand - strand |
| BXH6/Cub + strand - strand | HXB1/Ipcv + strand - strand | HXB17/Ipcv + strand - strand | HXB29/Ipcv + strand - strand |
| BXH8/Cub + strand - strand | |||
Kidney Strain Specific Reads Counts (Total/Not Sampled) - Show Individual Tracks
| HXB/BXH Strains | |||
|---|---|---|---|
| BN-Lx/Cub + strand - strand | BXH11/Cub + strand - strand | HXB7/Ipcv + strand - strand | HXB23/Ipcv + strand - strand |
| SHR/OlaIpcv + strand - strand | BXH12/Cub + strand - strand | HXB10/IpcvMcwi + strand - strand | HXB24/Ipcv + strand - strand |
| BXH2/CubMcwi + strand - strand | BXH13/Cub + strand - strand | HXB13/Ipcv + strand - strand | HXB25/Ipcv + strand - strand |
| BXH3/CubMcwi + strand - strand | HXB1/Ipcv + strand - strand | HXB15/Ipcv + strand - strand | HXB27/Ipcv + strand - strand |
| BXH6/Cub + strand - strand | HXB2/IpcvMcwi + strand - strand | HXB17/Ipcv + strand - strand | HXB29/Ipcv + strand - strand |
| BXH8/Cub + strand - strand | HXB3/Ipcv + strand - strand | HXB18/Ipcv + strand - strand | HXB31/IpcvMcwi + strand - strand |
| BXH9/Cub + strand - strand | HXB4/IpcvMcwi + strand - strand | HXB21/Ipcv + strand - strand | |
| BXH10/Cub + strand - strand | HXB5/Ipcv + strand - strand | HXB22/Ipcv + strand - strand | |
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