About the data

Cao 2017 L2 Larva Dataset (reprocessed)

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 2019 Embryogenesis Dataset

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 2019 Neuron Dataset

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 2020 L2 dataset

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 2020 Neuron Dataset

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