Molecular pathways of learning in the single-celled ciliate Stentor coeruleus
Data files
Apr 21, 2026 version files 414.90 GB
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B1a_S910_L001_I1_001.fastq.gz
605.56 MB
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B1a_S910_L001_R1_001.fastq.gz
6.46 GB
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B1a_S910_L001_R2_001.fastq.gz
6.52 GB
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B1b_S911_L001_I1_001.fastq.gz
419.65 MB
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B1b_S911_L001_R1_001.fastq.gz
4.65 GB
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B1b_S911_L001_R2_001.fastq.gz
4.71 GB
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B1c_S912_L001_I1_001.fastq.gz
526.22 MB
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B1c_S912_L001_R1_001.fastq.gz
5.84 GB
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B1c_S912_L001_R2_001.fastq.gz
5.92 GB
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B2a_S913_L001_I1_001.fastq.gz
354.08 MB
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B2a_S913_L001_R1_001.fastq.gz
4.45 GB
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B2a_S913_L001_R2_001.fastq.gz
4.52 GB
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B2b_S914_L001_I1_001.fastq.gz
506.29 MB
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B2b_S914_L001_R1_001.fastq.gz
5.70 GB
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B2b_S914_L001_R2_001.fastq.gz
5.76 GB
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B2c_S915_L001_I1_001.fastq.gz
439.65 MB
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B2c_S915_L001_R1_001.fastq.gz
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B2c_S915_L001_R2_001.fastq.gz
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B3a_S916_L001_I1_001.fastq.gz
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B3a_S916_L001_R1_001.fastq.gz
5.84 GB
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B3a_S916_L001_R2_001.fastq.gz
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B3b_S917_L001_I1_001.fastq.gz
495.57 MB
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B3b_S917_L001_R1_001.fastq.gz
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B3b_S917_L001_R2_001.fastq.gz
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B3c_S918_L001_I1_001.fastq.gz
361.89 MB
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B3c_S918_L001_R1_001.fastq.gz
4.56 GB
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B3c_S918_L001_R2_001.fastq.gz
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R1a_S901_L001_I1_001.fastq.gz
524.94 MB
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R1a_S901_L001_R1_001.fastq.gz
6 GB
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R1a_S901_L001_R2_001.fastq.gz
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R1b_S902_L001_I1_001.fastq.gz
557.74 MB
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R1b_S902_L001_R1_001.fastq.gz
6.12 GB
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R1b_S902_L001_R2_001.fastq.gz
6.15 GB
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R1c_S903_L001_I1_001.fastq.gz
452.96 MB
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R1c_S903_L001_R1_001.fastq.gz
5.69 GB
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R1c_S903_L001_R2_001.fastq.gz
5.75 GB
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R2a_S904_L001_I1_001.fastq.gz
522.99 MB
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R2a_S904_L001_R1_001.fastq.gz
5.80 GB
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R2a_S904_L001_R2_001.fastq.gz
5.83 GB
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R2b_S905_L001_I1_001.fastq.gz
442.45 MB
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R2b_S905_L001_R1_001.fastq.gz
4.85 GB
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R2b_S905_L001_R2_001.fastq.gz
4.89 GB
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R2c_S906_L001_I1_001.fastq.gz
586.68 MB
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R2c_S906_L001_R1_001.fastq.gz
6.09 GB
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R2c_S906_L001_R2_001.fastq.gz
6.12 GB
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R3a_S907_L001_I1_001.fastq.gz
428.86 MB
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R3a_S907_L001_R1_001.fastq.gz
5.21 GB
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R3a_S907_L001_R2_001.fastq.gz
5.27 GB
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R3b_S908_L001_I1_001.fastq.gz
374.44 MB
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R3b_S908_L001_R1_001.fastq.gz
4.71 GB
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R3b_S908_L001_R2_001.fastq.gz
4.75 GB
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R3c_S909_L001_I1_001.fastq.gz
386.75 MB
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R3c_S909_L001_R1_001.fastq.gz
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R3c_S909_L001_R2_001.fastq.gz
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README.md
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rna_exp2.zip
209.83 GB
Abstract
How can a single cell learn without a brain? Although learning and memory are often viewed as unique features of animals with complex nervous systems, single-celled organisms also demonstrate basic forms of learning and memory. The giant single cell Stentor coeruleus responds to mechanical stimuli by contracting into a compact shape. When a Stentor cell is repeatedly stimulated at a constant level of force, it will habituate and learn to ignore that stimulus but will still respond to stronger stimuli. Here, we explored the molecular changes that occur during the formation of this cellular memory in order to improve our understanding of non-synaptic learning. RNA sequencing identified candidate proteins and genes that change over the course of learning and forgetting. These candidates point towards the regulation of Stentor learning by calcium signaling and protein phosphorylation. Ultimately, these findings shed light on the origins of intelligence independent of complex multicellular circuitry.
Dataset DOI: 10.5061/dryad.z34tmpgrm
Description of the data and file structure
Stentor coeruleus is a model for studying learning in single cells because they undergo habituation after training with mechanical stimuli. We performed RNA sequencing on trained and untrained cells to identify transcriptomic changes during the process of unicellular learning. Annotation information can be found on https://stentor.ciliate.org/
We did experiments on monoculture cells, which were sourced from the same subculture of Stentor coeruleus cells, as well as experiments on polyculture cells, which were sourced from different subcultures. The monoculture data are in the individual files with the "monoculture" descriptor, while the polyculture cell data are located in the "rna_exp2" zip folder. Details about naming conventions and sample descriptions are included below each file name.
Files and variables
MONOCULTURE CELL DATASET
File: R1a_S901_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 19 hrs of training at 1 tap/min - first replicate
File: R1a_S901_L001_R1_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - first replicate (read 1)
File: R1a_S901_L001_R2_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - first replicate (read 2)
File: R1b_S902_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 19 hrs of training) - first replicate
File: R1b_S902_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - first replicate (read 1)
File: R1b_S902_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - first replicate (read 2)
File: R1c_S903_L001_I1_001.fastq.gz
Description: index file; monoculture cells remained on bench without training for 19 hrs - first replicate
File: R1c_S903_L001_R1_001.fastq.gz
Description: monoculture cells remained on the bench without training for 19 hrs - first replicate (read 1)
File: R1c_S903_L001_R2_001.fastq.gz
Description: monoculture cells remained on the bench without training for 19 hrs - first replicate (read 2)
File: R2a_S904_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 19 hrs of training at 1 tap/min - second replicate
File: R2a_S904_L001_R1_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - second replicate (read 1)
File: R2a_S904_L001_R2_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - second replicate (read 2)
File: R2b_S905_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 19 hrs of training) - second replicate
File: R2b_S905_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - second replicate (read 1)
File: R2b_S905_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - second replicate (read 2)
File: R2c_S906_L001_I1_001.fastq.gz
Description: index file; monoculture cells remained on bench without training for 19 hrs - second replicate
File: R2c_S906_L001_R1_001.fastq.gz
Description: monoculture cells remained on the bench without training for 19 hrs - second replicate (read 1)
File: R2c_S906_L001_R2_001.fastq.gz
Description: monoculture cells remained on the bench without training for 19 hrs - second replicate (read 2)
File: R3a_S907_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 19 hrs of training at 1 tap/min - third replicate
File: R3a_S907_L001_R1_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - third replicate (read 1)
File: R3a_S907_L001_R2_001.fastq.gz
Description: monoculture cells underwent 19 hrs of training at 1 tap/min - third replicate (read 2)
File: R3b_S908_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 19 hrs of training) - third replicate
File: R3b_S908_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - third replicate (read 1)
File: R3b_S908_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - third replicate (read 2)
File: R3c_S909_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 19 hrs of training) - third replicate
File: R3c_S909_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - third replicate (read 1)
File: R3c_S909_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 19 hrs of training) - third replicate (read 2)
File: B1a_S910_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - first replicate
File: B1a_S910_L001_R1_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - first replicate (read 1)
File: B1a_S910_L001_R2_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - first replicate (read 2)
File: B1b_S911_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 4 hrs of training) - first replicate
File: B1b_S911_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - first replicate (read 1)
File: B1b_S911_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - first replicate (read 2)
File: B1c_S912_L001_I1_001.fastq.gz
Description: index file; monoculture cells remained on bench without training for 4 hrs - first replicate
File: B1c_S912_L001_R1_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - first replicate (read 1)
File: B1c_S912_L001_R2_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - first replicate (read 2)
File: B2a_S913_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - second replicate
File: B2a_S913_L001_R1_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - second replicate (read 1)
File: B2a_S913_L001_R2_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - second replicate (read 2)
File: B2b_S914_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 4 hrs of training) - second replicate
File: B2b_S914_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - second replicate (read 1)
File: B2b_S914_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - second replicate (read 2)
File: B2c_S915_L001_I1_001.fastq.gz
Description: index file; monoculture cells remained on bench without training for 4 hrs - second replicate
File: B2c_S915_L001_R1_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - second replicate (read 1)
File: B2c_S915_L001_R2_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - second replicate (read 2)
File: B3a_S916_L001_I1_001.fastq.gz
Description: index file; monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - third replicate
File: B3a_S916_L001_R1_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - third replicate (read 1)
File: B3a_S916_L001_R2_001.fastq.gz
Description: monoculture cells underwent 4 hrs of training at 1 tap/1.2 sec - third replicate (read 2)
File: B3b_S917_L001_I1_001.fastq.gz
Description: index file; time 0 for monoculture cells (before 4 hrs of training) - third replicate
File: B3b_S917_L001_R1_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - third replicate (read 1)
File: B3b_S917_L001_R2_001.fastq.gz
Description: time 0 for monoculture cells (before 4 hrs of training) - third replicate (read 2)
File: B3c_S918_L001_I1_001.fastq.gz
Description: index file; monoculture cells remained on bench without training for 4 hrs - third replicate
File: B3c_S918_L001_R1_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - third replicate (read 1)
File: B3c_S918_L001_R2_001.fastq.gz
Description: monoculture cells remained on the bench without training for 4 hrs - third replicate (read 2)
POLYCULTURE CELL DATASET
File: rna_exp2.zip
Description:
| Sample name | Experimental paradigm |
|---|---|
| DR4876_01 | Trained for 19 hrs |
| DR4876_02 | Time 0 |
| DR4876_03 | No training for 19 hrs |
| DR4876_04 | Trained for 19 hrs |
| DR4876_05 | Time 0 |
| DR4876_06 | No training for 19 hrs |
| DR4876_07 | Trained for 19 hrs |
| DR4876_08 | Time 0 |
| DR4876_09 | No training for 19 hrs |
| DR4876_10 | Trained for 19 hrs + 10 min forgetting |
| DR4876_11 | No training for 19 hrs + 10 min |
| DR4876_12 | Trained for 19 hrs + 10 min forgetting |
| DR4876_13 | No training for 19 hrs + 10 min |
| DR4876_14 | Trained for 19 hrs + 10 min forgetting |
| DR4876_15 | No training for 19 hrs + 10 min |
| DR4876_16 | Trained for 19 hrs + 90 min forgetting |
| DR4876_17 | No training for 20.5 hrs |
| DR4876_18 | Trained for 19 hrs + 90 min forgetting |
| DR4876_19 | No training for 20.5 hrs |
| DR4876_20 | Trained for 19 hrs + 90 min forgetting |
| DR4876_21 | No training for 20.5 hrs |
Descriptors in file titles:
I1 = index file
R1 = read 1
R2 = read 2
Code/software
We used Kallisto to generate a reference index for Stentor coeruleus and quantify transcript abundance. Data were processed and analyzed with custom scripts in Python and R, which are available here: https://github.com/aralbright/2025_stentor_learning/
Access information
Other publicly accessible locations of the data:
- N/A
Data was derived from the following sources:
- N/A