Click on the file below to download a table of retroelements pertaining to that context
Data and code used to generate the retro-transcriptome
across non-diseased tissues, cancer, and embryogenesis:
Sample Code:
Raw RNA-sequencing Folders
Normalized RNA-sequencing Folders
Click on the dataset listed above to download the associated zip folder (in each file, annotated genes are on the top, retroelements are on the bottom)
The Raw folders will download a folder with:
- Raw_counts.csv: This file contains the raw counts, generated by aggregating the individual files from the GDC and Telescope pipelines
The Normalized folders will download a folder with:
- TPM_counts.csv: This file contains the TPM normalized counts. For ease of use, we replaced the GSM or SRR identifiers with the sample names. The original identifiers can be found in the Raw_counts.csv file
- Filtered_TPM_counts.csv: This file contains the filtered annotated genes and retroelements (TPM > 1 in at least one sample)
NOTE: The RNA Atlas (GSE138734) has sequencing data from tissues, cell-types, and cell lines. To enable ease of use, we created a csv file for each one broad category. To reduce the file size for the RNA Atlas TPM files, we averaged the technical replicates for each sample into a single column (the Raw_counts file still contains all 4105 samples). For the other studies, all of the technical or biological replicates are maintained as separate columns. For assistance in analyzing or interpreting these files, please contact us at: [email protected].