SMED30008463

Overview
NameSMED30008463
Smed IDSMED30008463
Length (bp)396
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 SMED30008463 (SMED30008463) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008463 (SMED30008463) 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 SMED30008463 (SMED30008463) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008463 (SMED30008463) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30008463

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior sideSMED30008463h1SMcG0017128 dd_Smed_v4_5221_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30008463h1SMcG0017128 dd_Smed_v4_5221_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
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BLAST of SMED30008463 vs. TrEMBL
Match: A0A195FUE3 (Uncharacterized protein OS=Trachymyrmex septentrionalis OX=34720 GN=ALC56_01647 PE=4 SV=1)

HSP 1 Score: 105.145 bits (261), Expect = 1.809e-26
Identity = 52/72 (72.22%), Postives = 57/72 (79.17%), Query Frame = 1 
Query:  127 LTNLKHYSDHILKSDVYFNKPTTTRVL*KEIKRCIYEIQPHLCKMVMRNFDKRVRMCQQSRVDYLPDVLFHK 342
            LT+L  +    LKS VY NKPTTTR L +EI+RCI EIQPHLCKMVM NFDKRVRMC QSR  +LPDVLFHK
Sbjct:   56 LTSLDFFLWGYLKSQVYVNKPTTTRALKEEIQRCINEIQPHLCKMVMENFDKRVRMCMQSRGGHLPDVLFHK 127
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BLAST of SMED30008463 vs. TrEMBL
Match: A0A195EWS3 (Uncharacterized protein (Fragment) OS=Trachymyrmex septentrionalis OX=34720 GN=ALC56_13191 PE=4 SV=1)

HSP 1 Score: 100.523 bits (249), Expect = 2.604e-25
Identity = 50/71 (70.42%), Postives = 55/71 (77.46%), Query Frame = 1 
Query:  127 LTNLKHYSDHILKSDVYFNKPTTTRVL*KEIKRCIYEIQPHLCKMVMRNFDKRVRMCQQSRVDYLPDVLFH 339
            LT L  +    LKS VY N+PTTTR L +EI+RCI EIQPHLCKMVM NFDKRVRMC QSR  +LPDVLFH
Sbjct:    3 LTPLDFFLWGYLKSQVYVNEPTTTRALKEEIQRCINEIQPHLCKMVMENFDKRVRMCMQSRGGHLPDVLFH 73
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BLAST of SMED30008463 vs. TrEMBL
Match: A0A088AEH7 (Uncharacterized protein OS=Apis mellifera OX=7460 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 1.343e-20
Identity = 45/72 (62.50%), Postives = 52/72 (72.22%), Query Frame = 1 
Query:  127 LTNLKHYSDHILKSDVYFNKPTTTRVL*KEIKRCIYEIQPHLCKMVMRNFDKRVRMCQQSRVDYLPDVLFHK 342
            LT L  +    LKS VY N PT TR L +EIKRCI EIQP LC+ VM+NFD+RVRMCQQ    +LP+VLFHK
Sbjct:   52 LTPLDFFLWSYLKSKVYVNNPTITRALQEEIKRCINEIQPQLCRKVMKNFDERVRMCQQIHGSHLPNVLFHK 123
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BLAST of SMED30008463 vs. TrEMBL
Match: E2BXR1 (Uncharacterized protein (Fragment) OS=Harpegnathos saltator OX=610380 GN=EAI_03467 PE=4 SV=1)

HSP 1 Score: 86.6557 bits (213), Expect = 5.500e-20
Identity = 41/60 (68.33%), Postives = 48/60 (80.00%), Query Frame = 1 
Query:  157 ILKSDVYFNKPTTTRVL*KEIKRCIYEIQPHLCKMVMRNFDKRVRMCQQSRVDYLPDVLF 336
            ILKS VY NKPT T  L ++I+RCI EIQPHLCK VM NF+KRV MCQQ+R  +LPD+LF
Sbjct:    1 ILKSKVYTNKPTATHALKEKIERCINEIQPHLCKTVMENFNKRVHMCQQNRGVHLPDMLF 60
[Close]
BLAST of SMED30008463 vs. TrEMBL
Match: A0A151K0K8 (Uncharacterized protein (Fragment) OS=Trachymyrmex septentrionalis OX=34720 GN=ALC56_02448 PE=4 SV=1)

HSP 1 Score: 87.0409 bits (214), Expect = 1.352e-19
Identity = 51/106 (48.11%), Postives = 57/106 (53.77%), Query Frame = 1 
Query:  127 LTNLKHYSDHILKSDVYFNKPTTTRVL*KEIKRCIYEIQPHLCKMVMRNFDKRVRMCQQS----------------------------------RVDYLPDVLFHK 342
            +T+L  +    LKS VY NKPTTTR L +EI+RCI EIQPHLCKMVM NFDKRVRMC QS                                  R  +LPDVLFHK
Sbjct:    1 ITSLDFFLWGYLKSQVYVNKPTTTRALKEEIQRCINEIQPHLCKMVMENFDKRVRMCMQSXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRGGHLPDVLFHK 106
The following BLAST results are available for this feature:
BLAST of SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A195FUE31.809e-2672.22Uncharacterized protein OS=Trachymyrmex septentrio... [more]
A0A195EWS32.604e-2570.42Uncharacterized protein (Fragment) OS=Trachymyrmex... [more]
A0A088AEH71.343e-2062.50Uncharacterized protein OS=Apis mellifera OX=7460 ... [more]
E2BXR15.500e-2068.33Uncharacterized protein (Fragment) OS=Harpegnathos... [more]
A0A151K0K81.352e-1948.11Uncharacterized protein (Fragment) OS=Trachymyrmex... [more]
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BLAST of SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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 SMED30008463 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

>SMED30008463 ID=SMED30008463|Name=SMED30008463|organism=Schmidtea mediterranea sexual|type=transcript|length=396bp
TTACAATTCCGTAATCAGAATAAATGTTCTCAATGCGGTATAAGTATAGA
ACTTGTAACTTATGGTAAAGGCGGACTCATGCAAGGACAATCTGCTAGAT
TCAACCGGACAAGAAATCCAAAAATTTTGACGAACTTAAAACACTATTCT
GATCATATTTTAAAGTCAGATGTCTATTTCAACAAGCCTACAACCACCCG
TGTATTATAGAAGGAAATTAAACGCTGCATCTACGAAATTCAGCCACATT
TATGCAAAATGGTCATGAGAAATTTCGACAAAAGAGTGCGTATGTGTCAA
CAAAGCCGTGTAGACTATTTGCCCGATGTTTTATTCCATAAATAATCCTA
TGTACTTTATGATTCAATAAAAAAATAAAAGACTAAAAAGATCGGA
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