SMED30023176

Overview
NameSMED30023176
Smed IDSMED30023176
Length (bp)150
Neoblast Clusters

Zeng et. al., 2018




 



 

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




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30023176

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023176h1SMcG0000618 dd_Smed_v4_18201_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023176 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011030:198..346 -745
v31.019718:1576..1724 -736
Homology
BLAST of SMED30023176 vs. Planmine SMEST
Match: SMESG000015256.1 (SMESG000015256.1)

HSP 1 Score: 77.0258 bits (188), Expect = 9.900e-19
Identity = 49/50 (98.00%), Postives = 50/50 (100.00%), Query Frame = -1
Query:    1 FGMDSEQHXXXXXXXXXXXKSLKYIQKLQENKENVARIFSEWRSVGLVLD 150
            FGMDSEQHKKICKDVKVIVKSLKYIQKLQENKENV+RIFSEWRSVGLVLD
Sbjct:  436 FGMDSEQHKKICKDVKVIVKSLKYIQKLQENKENVSRIFSEWRSVGLVLD 485          
BLAST of SMED30023176 vs. Planmine SMEST
Match: SMESG000015256.1 (SMESG000015256.1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.077e-18
Identity = 49/50 (98.00%), Postives = 50/50 (100.00%), Query Frame = -1
Query:    1 FGMDSEQHXXXXXXXXXXXKSLKYIQKLQENKENVARIFSEWRSVGLVLD 150
            FGMDSEQHKKICKDVKVIVKSLKYIQKLQENKENV+RIFSEWRSVGLVLD
Sbjct:  463 FGMDSEQHKKICKDVKVIVKSLKYIQKLQENKENVSRIFSEWRSVGLVLD 512          
BLAST of SMED30023176 vs. Planmine SMEST
Match: SMESG000040082.1 (SMESG000040082.1)

HSP 1 Score: 45.0542 bits (105), Expect = 2.102e-7
Identity = 20/29 (68.97%), Postives = 23/29 (79.31%), Query Frame = -1
Query:    1 LKYIQKLQENKENVARIFSEWRSVGLVLD 87
            L +IQK  ENKE V +I SEWR+VGLVLD
Sbjct:  611 LTFIQKTNENKERVNKIVSEWRAVGLVLD 639          
The following BLAST results are available for this feature:
BLAST of SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 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 SMED30023176 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000015256.19.900e-1998.00SMESG000015256.1[more]
SMESG000015256.11.077e-1898.00SMESG000015256.1[more]
SMESG000040082.12.102e-768.97SMESG000040082.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023176 ID=SMED30023176|Name=SMED30023176|organism=Schmidtea mediterranea sexual|type=transcript|length=150bp
GTCAAGAACAAGGCCAACACTGCGCCATTCAGAGAAAATCCTTGCAACAT
TTTCTTTGTTTTCTTGTAATTTTTGGATATATTTCAAAGATTTTACTATG
ACCTTGACGTCTTTGCAGATTTTCTTATGTTGTTCACTATCCATTCCAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron