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Series GSE186036 Query DataSets for GSE186036
Status Public on Oct 20, 2021
Title Modular, Cascade-like Transcriptional Program of Regeneration in Stentor
Organism Stentor coeruleus
Experiment type Expression profiling by high throughput sequencing
Summary The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis at the level of a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half will regenerate an intact cell, including a new oral apparatus in the posterior half. We used RNAseq to assay the dynamic changes in Stentor’s transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression. By comparing transcriptional profiles of different regeneration events in the same species, we were able to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides new insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.
 
Overall design RNA-seq time series of regeneration paradigms in Stentor: 1. sucrose-shocked-induced OA regeneration (10 timepoints, 4 replicates) 2. sucrose-shocked-induced OA regeneration in the presence of cycloheximide ( 5 timepoints, 3 replicates) or in the presence of DMSO (5 timepoints, 3 replicates) 3. bisected cells (anterior and posterior fragments both assayed -- 6 timepoints 3 replicates)
 
Contributor(s) Sood P, Marshall W, Lin A, McGillivary R
Citation(s) 35924891
Submission date Oct 18, 2021
Last update date Aug 24, 2022
Contact name Wallace Marshall
E-mail(s) wallace.ucsf@gmail.com
Organization name UCSF
Street address 600 16th St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (2)
GPL30870 Illumina HiSeq 2500 (Stentor coeruleus)
GPL30871 Illumina NovaSeq 6000 (Stentor coeruleus)
Samples (100)
GSM5629399 Oral apparatus pre sucrose shock rep 1
GSM5629400 Oral apparatus post sucrose shock (T=30min) rep 1
GSM5629401 Oral apparatus post sucrose shock (T=60min) rep 1
Relations
BioProject PRJNA772176
SRA SRP341884

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Supplementary file Size Download File type/resource
GSE186036_RAW.tar 605.2 Mb (http)(custom) TAR (of H5, JSON, TSV)
GSE186036_SteCoe_Trinity_assembled_transcriptome_for_GEO.fasta.gz 11.7 Mb (ftp)(http) FASTA
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Raw data are available in SRA
Processed data provided as supplementary file

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