Cao and friends. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 2017.
This was the first scRNAseq C. elegans data to be published. The single cell matrices used here were a newer version that was reprocessed and re-annotated and kindly provided by Robert Waterston and colleagues.
The technology used was sci-RNA seq. Two experiments with C. elegans at the L2 larval stage were performed with labels and cell counts as below. Their annotations define 117 cell types.
| Experiment name | Cells |
|---|---|
| L2_experiment_1 | 35480 |
| L2_experiment_2 | 507 |
Packer and friends. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science 2019.
In the paper supplements, the way the age of the embryos was defined is described as follows:
Around 250,000 L1 larvae were 29 plated onto four 100 mm petri plates seeded with NA22 bacteria and allowed to develop at 20 30 °C. As the worms reached the young adult stage, the population was closely monitored. When 31 about 20-30% of the adults had a single embryo in either arm of the gonad, worms were 32 subjected to hypochlorite treatment. The time hypochlorite was added to the worms was 33 considered t = 0.
They used 10x Genomics v2 chemistry to profile 89,701 cells, split as below. Their annotations define 183 cell types.
| Experiment name | Cells | Description |
|---|---|---|
| Waterston_400_minutes | 25875 | 400 minute synchronized embryos |
| Waterston_300_minutes | 17168 | 300 minute synchronized embryos |
| Murray_b01 | 12129 | mixed time point |
| Waterston_500_minutes_batch_2 | 11589 | 500 minute synchronized embryos, replicate 1 |
| Waterston_500_minutes_batch_1 | 10532 | 500 minute synchronized embryos, replicate 2 |
| Murray_r17 | 9363 | mixed time point |
| Murray_b02 | 3045 | mixed time point |
Taylor and friends. Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing. biorxiv 2019.
This is the first data release of the C. elegans Neuronal Gene Expression Map & Network (CeNGEN). The aim of the project is to establish a comprehensive gene expression atlas of an entire nervous system at single-neuron resolution, described in the announcement publication. Their website is cengen.org.
As described in their website: We are performing 10x single-cell RNA-Seq on FACS-isolated neurons. Using 52,412 sequenced cells, 109/118 neuronal classes have been identified and computationally assigned to a cluster based on their gene expression fingerprint (93 confidently, 16 tentatively), and 9/118 classes have not been annotated yet.
They used 10x Genomics v2 and v3 chemistry to profile 65,450 cells from L4 stage larvae, split as below. Their annotations define 133 cell types.
| Experiment name | Cells | Strain | Method | Cell Types Targeted |
|---|---|---|---|---|
| eat-4 | 12743 | OH9625 | 10xv2 | Glutamatergic neurons |
| acr-2 | 11719 | CZ631 | 10xv3 | Cholinergic ventral cord motor neurons |
| Pan | 9216 | OH10689 | 10xv2 | All neurons |
| unc-3 | 6165 | OH11746 | 10xv2 | Ventral cord motor neurons |
| tph-1_ceh-10 | 4810 | NC3580 | 10xv2 | Serotonergic neurons and AIY, RID, CAN |
| ift-20 | 4056 | OH11157 | 10xv2 | Ciliated sensory neurons |
| cho-1_2 | 3849 | NC3579 | 10xv2 | Cholinergic neurons |
| cho-1_2 | 3471 | NC3579 | 10xv2 | Cholinergic neurons |
| unc-47_2 | 3123 | NC3582 | 10xv2 | GABAergic neurons |
| ceh-34 | 2648 | NC3583 | 10xv3 | Pharyngeal neurons |
| nmr-1 | 2389 | NC3572 | 10xv2 | Motor circuit command interneurons |
| unc-47_1 | 1261 | NC3582 | 10xv2 | GABAergic neurons |
Ben-David and friends. Whole-organism mapping of the genetics of gene expression at cellular resolution biorxiv 2020.
In this dataset 5 separate 10x v2 lanes were run with about 10,000 L2 cells on each, each batch is a replicate. Their annotations define 99 cell types.
| Experiment name | Cells |
|---|---|
| F4_5 | 11633 |
| F4_4 | 11464 |
| F4_2 | 11424 |
| F4_1 | 11336 |
| F4_3 | 9651 |
Taylor and friends. Molecular topography of an entire nervous system. biorxiv 2019.
This is the second data release of the C. elegans Neuronal Gene Expression Map & Network (CeNGEN). The aim of the project is to establish a comprehensive gene expression atlas of an entire nervous system at single-neuron resolution, described in the announcement publication. Their website is cengen.org.
The data matrix used used here was from the original unfiltered 10x matrices as outputted by cellranger, I kept the same barcodes they kept but skipped the soupX processing step as I don't think removing background from the matrix itself is a sensible thing. The authors provide the raw data as outputted by Cell Ranger and filtered by Emptydrops is at this Dropbox link.
They used 10x Genomics v2 and v3 chemistry to profile 100,599 cells from L4 stage larvae, split as below. Their annotations define 133 cell types.
| dropbox_id | cell_types_targeted | experiment_code | strain | genotype | version10x | total_cells |
|---|---|---|---|---|---|---|
| 1806-ST-1 | All neurons | Pan-1 | OH10689 | otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV | v2 | 642 |
| 1806-ST-2 | All neurons | Pan-2 | OH10689 | otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV | v2 | 813 |
| 2658-ST-1 | GABAergic neurons | unc-47_1 | NC3582 | oxIs12 [unc-47p::GFP + lin-15(+)] X; otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV | v2 | 185 |
| 2966-ST-1 | GABAergic neurons | unc-47_2 | NC3582 | oxIs12 [unc-47p::GFP + lin-15(+)] X; otIs355 [rab-3p(prom1)::2xNLS::tagRFP] IV | v2 | 290 |
| 3070-ST-1 | Motor circuit command interneurons | nmr-1 | NC3572 | akIs3 [nmr-1::GFP + lin-15(+)] V; otIs355 [rab-3p(prom1)::2x-NLS::tagRFP] IV | v2 | 1371 |
| 3131-ST-1 | Glutamatergic neurons | eat-4 | OH9625 | otIs292 [eat-4::mCherry + rol-6(su1006)] | v2 | 417 |
| 3183-ST-1 | Ventral cord motor neurons | unc-3 | OH11746 | pha-1(e2123) III; otIs447 [unc-3p::mCherry + pha-1(+)] IV | v2 | 724 |
| 3239-ST-1 | Ciliated sensory neurons | ift-20 | OH11157 | pha-1(e2123) III; otIs393 [ift-20::NLS::tagRFP + pha-1(+)] | v2 | 490 |
| 3441-ST-1 | Cholinergic neurons | cho-1_1 | NC3579 | otIs354 [cho-1(fosmid)::SL2::YFP::H2B]; otIs355 [rab-3(prom1)::2xNLS-tagRFP] IV | v2 | 507 |
| 3441-ST-2 | Cholinergic neurons | cho-1_2 | NC3579 | otIs354 [cho-1(fosmid)::SL2::YFP::H2B]; otIs355 [rab-3(prom1)::2xNLS-tagRFP] IV | v2 | 455 |
| 3465-ST-1 | Serotonergic neurons and AIY, RID, CAN | tph-1_ceh-10 | NC3580 | zdIs13 [tph-1p::GFP] IV; hpIs202 [ceh-10p::GFP + lin-15(+)] | v2 | 547 |
| 3495-ST-1 | Cholinergic ventral cord motor neurons | acr-2 | CZ631 | juIs14 [acr-2p::GFP + lin-15(+)] IV | v3 | 12133 |
| 3503-ST-1 | Pharyngeal neurons | ceh-34 | NC3583 | stIs10447 [ceh-34p::HIS-24::mCherry + unc-119(+)]; evIs111 [F25B3.3::GFP + dpy-20(+)] | v3 | 3345 |
| 3697-ST-1 | unc-86 expressing cells | unc-86 | CX5974 | unc-86::myr-GFP + odr-1::RFP] IV | v3 | 3506 |
| 3831-ST-1 | unc-53 expressing cells | unc-53 | NC3636 | hdIs1 [unc-53p::GFP + rol-6(su1006)]; otIs355 [rab-3prom1::2xNLS-tagRFP] IV | v3 | 5141 |
| 4138-ST-1 | PVT, nlp-13 expressing cells, I3, M3, NSM | nlp-13_ceh-2 | OH16007 + PS3504 | otIs742 [nlp-13p::GFP + lin-15(+)]. syIs54 [ceh-2::GFP + unc-119(+)]; unc-119 (ed4) | v3 | 9024 |
| 4170-ST-1 | M4, dopamine neurons, touch receptor neurons, O2-sensing neurons, SAB | ceh-28_dat-1 | nIs175 + NC3635 + NC3523 | nIs175 [ceh-28p::4xNLS-GFP + lin-15(+)]. NC3635 egIs1 [dat-1p::GFP]; uIs152 [mec-3::RFP]; kyEx1162 [gcy-35p::GFP]. wdIs90 [unc-4c::GFP] | v3 | 7370 |