Talks and presentations
International C. elegans meeting 2021
Talk from Erdem Varol: A computational approach linking neuron-specific gene expression with connectivity.Download
Recorded version available at: https://www.youtube.com/watch?v=1K1f8TJf8ic
Poster from Alec Barrett: Integrating bulk and single cell transcriptomics for accurate detection of tissue-specific gene expression. Download
International C. elegans meeting 2019
Datasets
160 bulk samples (covering 41 neuron types) were integrated with the single-cell data (see below) to improve accuracy. Integrated counts contain fewer samples and cell types than either source: cell types were included only if there were > 1 replicate for both sources, and the number of replicates in the integrated data is equal to the lower number of replicates in either source. The datasets are:
- Normalized and integrated gene counts (143 replicates, computed from the two datasets below)
- Raw gene counts for 160 bulk samples
- Single-cell pseudobulk counts (aggregated by biological replicate)
- Gene-level metadata
The single-cell sequencing data is available under several formats:
- The raw reads are available on GEO (GSE 136049).
- Full dataset (100,955 cells) as a Seurat (500 MB), Seurat v5 (500 MB) or Monocle (300 MB) object. Also available on Dropbox.
- Only the cells annotated as neurons (70,296 cells) as Seurat (4 GB) or Monocle (300 MB) object. Also available on Dropbox.
- For binary expression patterns, csv files are available for thresholds 1 (most permissive), 2 (medium), 3 (more conservative), and 4 (most stringent), here or on Dropbox. In these matrices, a gene determined not expressed in a cell has a value of 0, a gene above the threshold has a value >0 (the average TPM per gene per neuron type, as calculated by the monocle3 package).
In addition,
- The gene models used for alignment were based on the Wormbase WS273 GTF with extended 3’UTRs. These updated gene models are included with the single-cell GEO dataset.
- For comparison of scRNA-Seq and bulk RNA-Seq, 29 samples corresponding to 8 neuron classes were also described in the paper. The raw reads are uploaded on GEO (GSE169137), and the count matrix can be downloaded here.
Older Datasets are also available on https://www.dropbox.com/sh/ewq7cu7sbjixfb4/AABO5Vv5rR-mK02Jble77TCka