SMED30032887

Overview
NameSMED30032887
Smed IDSMED30032887
Length (bp)905
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of SMED30032887 (SMED30032887) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30032887 (SMED30032887) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of SMED30032887 (SMED30032887) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30032887 (SMED30032887) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Alignments
SMED30032887 aligns in the following genomic locations:
Alignment LocationAlignment Score
Schmidtea_mediterranea_mt_genome:15835..16739 -4525
Homology
BLAST of SMED30032887 vs. TrEMBL
Match: I1ZIG6 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 95.5153 bits (236), Expect = 1.044e-21
Identity = 46/46 (100.00%), Postives = 46/46 (100.00%), Query Frame = -1
Query:  768 NINPIPFVQWTVIQDKNQPDSHRSKLKSRIVLLVEQTKSKGLYTYL 905
            NINPIPFVQWTVIQDKNQPDSHRSKLKSRIVLLVEQTKSKGLYTYL
Sbjct:    1 NINPIPFVQWTVIQDKNQPDSHRSKLKSRIVLLVEQTKSKGLYTYL 46          
The following BLAST results are available for this feature:
BLAST of SMED30032887 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZIG61.044e-21100.00Uncharacterized protein (Fragment) OS=Schmidtea me... [more]
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BLAST of SMED30032887 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30032887 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30032887 ID=SMED30032887|Name=SMED30032887|organism=Schmidtea mediterranea sexual|type=transcript|length=905bp
gttagttgtaatattttcctttttgtattacggttcgtaggtatttttat
gtttttattctctcgaatggaatatgatatatcttttgtgtgttttgttt
tattttctttggttaacattagaattacattgattggtagtagtgatatg
ttttcggatttctttatctagtttttagttgtctttaggttaagcttttg
ttttacttgtttttttgtcctatttgtttaagttattcttaatagtattt
cttttaatcgttaaagatttgttagtcttctgtttgtttatatggttttt
agtaattctttttagcaattacgtaattaatatgaattatgctatatata
actcaatgcgtctacaactgttttctaaaaacatttcattttttgtaaaa
tgtagtccctgctcactgataagttaaatagctgcagtactttgactgta
cgaaggtagcataattacttgtctattaattctagaattgtttgaatggg
tttattgatagatagcaagttttatttagtcttgttttttaatttatact
ttctgtaaagatacagtttgatatttcaaggacgaaaagaccctatagag
tttttaacttagtggtgtttcttactttagttatttgttggggtaacggt
atttcttttgagtacttatttattacattatgaacttccttagggataac
agggatatagaatcttggaggacatatcgaagattttgttttctacctcg
atgttgaattgtagttaaagataggtgtagaggcctttacttttagtctg
ttcgactaataatactattcgtgatttgagtttagaccgatgtgaatcag
gttggtttttatcctgaatcactgtccattgtacgaaaggaattggattg
atatt
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte