Child dataset 2 of 4 from: Single and half-cell RNA-sequencing in Stentor coeruleus control, beta-tubulin, and dynein knockdown cells
Data files
May 08, 2026 version files 167.94 GB
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con1A_S197_L006_R1_001.fastq.gz
3.57 GB
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con1A_S197_L006_R2_001.fastq.gz
3.79 GB
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con1P_S198_L006_R1_001.fastq.gz
9.08 GB
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con1P_S198_L006_R2_001.fastq.gz
9.46 GB
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con2A_S199_L006_R1_001.fastq.gz
7.23 GB
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con2A_S199_L006_R2_001.fastq.gz
7.65 GB
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con2P_S200_L006_R1_001.fastq.gz
6.11 GB
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con2P_S200_L006_R2_001.fastq.gz
6.55 GB
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con3A_S201_L006_R1_001.fastq.gz
8.87 GB
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con3A_S201_L006_R2_001.fastq.gz
9.50 GB
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con3P_S202_L006_R1_001.fastq.gz
8.59 GB
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con3P_S202_L006_R2_001.fastq.gz
8.96 GB
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con4A_S203_L006_R1_001.fastq.gz
11.20 GB
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con4A_S203_L006_R2_001.fastq.gz
11.72 GB
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con4P_S204_L006_R1_001.fastq.gz
6.05 GB
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con4P_S204_L006_R2_001.fastq.gz
6.40 GB
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con5A_S205_L006_R1_001.fastq.gz
11.20 GB
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con5A_S205_L006_R2_001.fastq.gz
11.82 GB
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con5P_S206_L006_R1_001.fastq.gz
9.87 GB
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con5P_S206_L006_R2_001.fastq.gz
10.31 GB
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metadata.csv
7.93 KB
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README.md
1.73 KB
Abstract
Stentor coeruleus is a giant single-celled ciliates that reach lengths of up to 1 mm. Because of their large size, these cells are easy to manipulate, and they also possess the ability to heal wounds and regenerate. These properties are ideal for investigating subcellular pattern formation, as we can physically dissect the cells into anterior and posterior halves. We used half-cell RNA-sequencing to assay for changes in transcript skew along the cell's anterior-posterior axis upon knocking down beta-tubulin, an important component of the microtubule cytoskeleton, and dynein intermediate chains, a component of the molecular motor.
Dataset DOI: 10.5061/dryad.9zw3r22r0
These RNA sequencing data accompany our preprint:
Genome-wide analysis of anterior-posterior mRNA regionalization in Stentor coeruleus reveals a role for the microtubule cytoskeleton
Link: https://www.biorxiv.org/content/10.1101/2023.01.09.523364v4
metadata.csv contains file name, which experiment the file is from (bulk, tubulin, or dynein), condition (control or knockdown), region (anterior or posterior), and biological replicate.
Description of the data and file structure
Additional Dataset 2 of 4.
Each file is named for a treatment (con/control, tub/tubulin, G04/dynein construct #1, G05/dynein construct #2) and for which half of the cell (A/anterior, P/posterior) the fragment came from.
Dynein:
control:
con1A_S197_L006_R1_001.fastq.gz
con1A_S197_L006_R2_001.fastq.gz
con1P_S198_L006_R1_001.fastq.gz
con1P_S198_L006_R2_001.fastq.gz
con2A_S199_L006_R1_001.fastq.gz
con2A_S199_L006_R2_001.fastq.gz
con2P_S200_L006_R1_001.fastq.gz
con2P_S200_L006_R2_001.fastq.gz
con3A_S201_L006_R1_001.fastq.gz
con3A_S201_L006_R2_001.fastq.gz
con3P_S202_L006_R1_001.fastq.gz
con3P_S202_L006_R2_001.fastq.gz
con4A_S203_L006_R1_001.fastq.gz
con4A_S203_L006_R2_001.fastq.gz
con4P_S204_L006_R1_001.fastq.gz
con4P_S204_L006_R2_001.fastq.gz
con5A_S205_L006_R1_001.fastq.gz
con5A_S205_L006_R2_001.fastq.gz
con5P_S206_L006_R1_001.fastq.gz
con5P_S206_L006_R2_001.fastq.gz
See parent entry for details: https://doi.org/10.6078/D1WT6W
After conducting RNAi knockdown of beta-tubulin or dynein in Stentor coeruleus, we bisected the cells using a glass needle. Within 20 minutes of bisection, the whole cells and bisected cells were lysed and prepped for sequencing with the NEBNext Single Cell/Low Input Library Prep Kit for Illumina (Cat. No. E6420). Samples were pooled and submitted for sequencing on an Illumina NovaSeq6000 (SP200) or NovaSeqX (SP300).
See parent entry for details: https://doi.org/10.6078/D1WT6W