SMED30035838

Overview
NameSMED30035838
Smed IDSMED30035838
Length (bp)442
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 SMED30035838 (SMED30035838) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30035838 (SMED30035838) 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 SMED30035838 (SMED30035838) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30035838 (SMED30035838) 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




SMED30035838

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30035838h1SMcG0018115 dd_Smed_v4_10259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30035838h1SMcG0018115 Contig38164newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30035838h1SMcG0018115 Contig38164uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
protonephridiaSMED30035838h1SMcG0018115 Contig12938uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
protonephridiaSMED30035838h1SMcG0018115 Contig12938newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30035838h1SMcG0018115 Contig12938uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30035838h1SMcG0018115 Contig12938newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30035838h1SMcG0018115 Contig12938uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30035838h1SMcG0018115 Contig12938newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30035838h1SMcG0018115 dd_Smed_v4_10259_0_1dd_Smed_v4PMID:30962434
Cote et al., 2019
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30035838 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000218:202383..202878 +2191
Homology
BLAST of SMED30035838 vs. TrEMBL
Match: T1D158 (ADAMTS5 OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 7.326e-6
Identity = 32/99 (32.32%), Postives = 51/99 (51.52%), Query Frame = 1
Query:  133 NVKLQFIQPKISSL-ISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQ--------TRNNRCQFTGFVNKSQEMHGQFNLCKGIVSL*FLFSKTFL 402
            N K  FI+PK+ ++    +   +   SIE IK I ++FE F   FI+ L Q        +R  +C FTG VN ++     FNLC G++ + +  +K + 
Sbjct:   28 NGKETFIKPKVLTIEFRGLSENSSILSIEKIKSIKYQFEVFNERFILNLRQHRYGLGKSSRQTQCHFTGNVNTNKYSGAHFNLCNGMIGVFYWNNKEYF 126          
BLAST of SMED30035838 vs. Planmine SMEST
Match: SMESG000038885.1 (SMESG000038885.1)

HSP 1 Score: 194.126 bits (492), Expect = 6.667e-58
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 1
Query:   85 NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI 366
            NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI
Sbjct:   17 NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI 110          
BLAST of SMED30035838 vs. Planmine SMEST
Match: SMESG000038885.1 (SMESG000038885.1)

HSP 1 Score: 192.971 bits (489), Expect = 1.050e-57
Identity = 94/94 (100.00%), Postives = 94/94 (100.00%), Query Frame = 1
Query:   85 NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI 366
            NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI
Sbjct:   17 NNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSVYNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEMHGQFNLCKGI 110          
The following BLAST results are available for this feature:
BLAST of SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
T1D1587.326e-632.32ADAMTS5 OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1[more]
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BLAST of SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 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 SMED30035838 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000038885.16.667e-58100.00SMESG000038885.1[more]
SMESG000038885.11.050e-57100.00SMESG000038885.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035838 ID=SMED30035838|Name=SMED30035838|organism=Schmidtea mediterranea sexual|type=transcript|length=442bp
TGATAAATTAGTTAATTTTTCATAATTATACTATAAATGTTATCGAGTGA
ACTAATATTGATTTCTATTGCTTTGTTGTCTGCAAATAATAACGGTCATC
TTATTGGAAAACAAGAACCTTCAAATACTACAAATGTCAAACTACAATTC
ATCCAACCAAAGATTTCGTCTCTGATTTCGTCTGTATATAATGCTACATT
TTATTCTTCTATAGAGAATATCAAACAAATCGCTTTTGAATTTGAAGCCT
TTCAATTATATTTTATAATTCAATTGAATCAAACTCGTAATAATAGATGC
CAATTTACTGGATTTGTAAACAAATCGCAAGAAATGCATGGACAATTCAA
TCTATGCAAAGGAATTGTAAGTTTGTAATTTTTGTTTAGTAAAACTTTTC
TAAACGTTATGTCGATGAAAGTGGAAACGTTCTTAAAATGAG
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protein sequence of SMED30035838-orf-1

>SMED30035838-orf-1 ID=SMED30035838-orf-1|Name=SMED30035838-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MLSSELILISIALLSANNNGHLIGKQEPSNTTNVKLQFIQPKISSLISSV
YNATFYSSIENIKQIAFEFEAFQLYFIIQLNQTRNNRCQFTGFVNKSQEM
HGQFNLCKGIVSL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004222metalloendopeptidase activity
GO:0008237metallopeptidase activity
GO:0008270zinc ion binding
GO:0046872metal ion binding
Vocabulary: cellular component
TermDefinition
GO:0005578proteinaceous extracellular matrix
Vocabulary: biological process
TermDefinition
GO:0006508proteolysis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..16
score: 0.526