SMED30014533

Overview
NameSMED30014533
Smed IDSMED30014533
Length (bp)789
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30014533 (SMED30014533) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014533 (SMED30014533) in cells (dots) of each of the 12 neoblast clusters.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30014533

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30014533h1SMcG0001807 dd_Smed_v4_3360_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014533h1SMcG0001807 dd_Smed_v4_3360_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30014533h1SMcG0001807 dd_Smed_v4_3360_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30014533h1SMcG0001807 dd_Smed_v4_3360_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30014533h1SMcG0001807 dd_Smed_v4_14688_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
Homology
BLAST of SMED30014533 vs. Planmine SMEST
Match: SMESG000023635.1 (SMESG000023635.1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.798e-7
Identity = 23/26 (88.46%), Postives = 25/26 (96.15%), Query Frame = -1
Query:   91 VYIGLSSGQLIDDFQNLRAESYPAVD 168
            ++ GLSSGQLIDDFQNLRAESYPAVD
Sbjct:  178 LHRGLSSGQLIDDFQNLRAESYPAVD 203          
BLAST of SMED30014533 vs. Planmine SMEST
Match: SMESG000023635.1 (SMESG000023635.1)

HSP 1 Score: 50.447 bits (119), Expect = 2.161e-7
Identity = 23/26 (88.46%), Postives = 25/26 (96.15%), Query Frame = -1
Query:   91 VYIGLSSGQLIDDFQNLRAESYPAVD 168
            ++ GLSSGQLIDDFQNLRAESYPAVD
Sbjct:  181 LHRGLSSGQLIDDFQNLRAESYPAVD 206          
BLAST of SMED30014533 vs. Planmine SMEST
Match: SMESG000023635.1 (SMESG000023635.1)

HSP 1 Score: 50.8322 bits (120), Expect = 2.287e-7
Identity = 23/26 (88.46%), Postives = 25/26 (96.15%), Query Frame = -1
Query:   91 VYIGLSSGQLIDDFQNLRAESYPAVD 168
            ++ GLSSGQLIDDFQNLRAESYPAVD
Sbjct:  196 LHRGLSSGQLIDDFQNLRAESYPAVD 221          
BLAST of SMED30014533 vs. Planmine SMEST
Match: SMESG000023635.1 (SMESG000023635.1)

HSP 1 Score: 50.447 bits (119), Expect = 2.629e-7
Identity = 23/26 (88.46%), Postives = 25/26 (96.15%), Query Frame = -1
Query:   91 VYIGLSSGQLIDDFQNLRAESYPAVD 168
            ++ GLSSGQLIDDFQNLRAESYPAVD
Sbjct:  199 LHRGLSSGQLIDDFQNLRAESYPAVD 224          
BLAST of SMED30014533 vs. Planmine SMEST
Match: SMESG000007021.1 (SMESG000007021.1)

HSP 1 Score: 44.669 bits (104), Expect = 7.641e-7
Identity = 24/53 (45.28%), Postives = 33/53 (62.26%), Query Frame = -1
Query:  367 KKISKHLGNLDYKIISN----------KSITAVGLCLCPVYQYSSNWCNSAFI 495
            +K+ K +GNL+YKI+SN          KS T VGLC   VYQ++ N CN+ +I
Sbjct:  295 RKLGKLIGNLEYKIVSNSCKVRNMFINKSKTPVGLCSDLVYQFTCNGCNATYI 347          

HSP 2 Score: 26.1794 bits (56), Expect = 7.641e-7
Identity = 14/38 (36.84%), Postives = 22/38 (57.89%), Query Frame = -3
Query:  497 SNCNLTNESK*IVDVNNIDSACENYRSKLVLVLSYSKG 610
            S CNL++  +  VD+ +  +  +    K VLVL YS+G
Sbjct:  252 SECNLSDGCELSVDLGDCKNGYKKIEPKYVLVLPYSEG 289          
The following BLAST results are available for this feature:
BLAST of SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 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 SMED30014533 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000023635.11.798e-788.46SMESG000023635.1[more]
SMESG000023635.12.161e-788.46SMESG000023635.1[more]
SMESG000023635.12.287e-788.46SMESG000023635.1[more]
SMESG000023635.12.629e-788.46SMESG000023635.1[more]
SMESG000007021.17.641e-745.28SMESG000007021.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014533 ID=SMED30014533|Name=SMED30014533|organism=Schmidtea mediterranea sexual|type=transcript|length=789bp
TTTTTTTTTTTTTTTTTTTTTACAAAAAAACTAATATTATATTTAACATT
TAAAATACATGAAACATACAAAAGATATCGTTAAAATTTAATCAACTGCT
GGATAAGATTCTGCACGGAGATTTTGAAAGTCATCAATAAGTTGACCACT
TGATAGACCTATATAGACGATTTTGATTTAATTTTTATCCAATTAAATAA
ATTTAATAATAATCAGTGAGCCAATGGTGCCTCAGTACATGGCACAAAAC
ACTAGAGGCTCCCTAATTTCAAATAAGGAATGATTTTTTTGTAATTAGTC
AGTTCGATTTTAAACTTAAAAATATTATATCTTTCAAAACATTTTACAGG
ATTTAAAATATATATATATAAATGCGGAATTACACCAATTGCTTGAATAT
TGATAAACGGGACACAAACACAATCCAACTGCAGTTATTGACTTATTAGA
AATGATTTTATAATCTAAATTTCCCAAGTGCTTGCTAATCTTCTTAACCT
TTCGAGTACGACAATACCAACACTAATTTAGACCTATAATTCTCACACGC
ACTATCGATGTTATTTACATCTACAATCTATTTACTTTCATTAGTCAAAT
TACAATTAGACATTCTTAAACTTTTATTAAGCTTTTCTTGTAATTAAATC
ATTACTTATTTTAAATGTTTATTATTTTATCCGCTGCGATGAAATTAATC
AATTTTTTTCTATTATAAAATTTCTTTTAAATAAAATAGAATTTTATAAC
ATTAAAATTGTTGGGGTTGTCGGTATTCGAATAGGAATT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell