REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Critical commercial assays | ||
TruSeq RNA Library Prep Kit v2 | https://emea.illumina.com/ | |
NEBNext Small RNA Library Prep Set | https://www.neb.com | |
Deposited data | ||
Small RNA sequencing (DRG) | dbGap | dbGap:phs001158 |
Total RNA Sequencing (DRG) | dbGap | dbGap:phs001158 |
Long and Small RNA sequencing iPSC-derived neurons | GEO Datasets | GSE161530 |
Raw Data files and analyzed files | Github | mouzkolit/NOCICEPTRA2Analysis (https://doi.org/10.5281/zenodo.10117927) |
NOCICEPTRA 2.0 Tool | Github | mouzkolit/NOCICEPTRA2.0 (https://doi.org/10.5281/zenodo.10117925) |
The Human Dorsal Root Ganglion Transcriptome | University of Texas at Dallas | MR 15-237 |
Software and algorithms | ||
excerpt v4.3.2 | GitHub: mouzkolit/nociceptra2_analysis | |
Salmon v0.13.1 | GitHub: muiphysiologie/NOCICEPTRA2.0, Streamlit: nociceptra.streamlit.app |
|
DESeq2 v1.40.2 | https://github.gersteinlab.org/exceRpt/ | |
WGCNA | https://salmon.readthedocs.io/en/latest/salmon.html | |
Ashr v2.2-63 | https://www.r-project.org/ | |
lncSEA v2.0 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
MR-microT | https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/ | |
DuckDB v0.6.0 | https://www.rdocumentation.org/packages/ashr/versions/2.0.5 |