SMED30011746

Overview
NameSMED30011746
Smed IDSMED30011746
Length (bp)565
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 SMED30011746 (SMED30011746) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011746 (SMED30011746) 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 SMED30011746 (SMED30011746) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011746 (SMED30011746) 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




SMED30011746

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
parenchymal cellSMED30011746SMESG000046847.1 dd_Smed_v4_5050_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011746SMESG000046847.1 dd_Smed_v6_5050_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30011746 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000906:44187..44789 -2256
Homology
BLAST of SMED30011746 vs. Ensembl Fly
Match: CG14483 (gene:FBgn0034248 transcript:FBtr0345525)

HSP 1 Score: 42.743 bits (99), Expect = 9.890e-6
Identity = 16/43 (37.21%), Postives = 27/43 (62.79%), Query Frame = -2
Query:  247 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMY 375
            MG W LEVA+M  Y++FPV  + +FN  ++      K ++++Y
Sbjct:    1 MGTWVLEVAKMGMYMAFPVTLFHLFNQPEYFEEWVTKKKRELY 43          
BLAST of SMED30011746 vs. Ensembl Fly
Match: CG14483 (gene:FBgn0034248 transcript:FBtr0086902)

HSP 1 Score: 42.743 bits (99), Expect = 9.890e-6
Identity = 16/43 (37.21%), Postives = 27/43 (62.79%), Query Frame = -2
Query:  247 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMY 375
            MG W LEVA+M  Y++FPV  + +FN  ++      K ++++Y
Sbjct:    1 MGTWVLEVAKMGMYMAFPVTLFHLFNQPEYFEEWVTKKKRELY 43          
BLAST of SMED30011746 vs. Ensembl Fly
Match: CG14483 (gene:FBgn0034248 transcript:FBtr0329863)

HSP 1 Score: 42.743 bits (99), Expect = 9.890e-6
Identity = 16/43 (37.21%), Postives = 27/43 (62.79%), Query Frame = -2
Query:  247 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMY 375
            MG W LEVA+M  Y++FPV  + +FN  ++      K ++++Y
Sbjct:    1 MGTWVLEVAKMGMYMAFPVTLFHLFNQPEYFEEWVTKKKRELY 43          
BLAST of SMED30011746 vs. TrEMBL
Match: A0A5K3ETX6 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 6.500e-6
Identity = 29/77 (37.66%), Postives = 44/77 (57.14%), Query Frame = -2
Query:  163 IFEILIMGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMYNELGIDFYSNDIVPLEEALAQKSIFDKL 393
            IF I +  GWK+E  R+  YLS P+A + + N    I +  N YR D+Y   G+D + +D+  + E L +K+  DKL
Sbjct:   59 IFHIDLTMGWKMESLRLGLYLSIPLAAFTMSNWPSVIDHYHNAYRLDVYGRTGVDVFPSDVDSI-ETLQKKA--DKL 132          
BLAST of SMED30011746 vs. TrEMBL
Match: A0A5B7HAC5 (Protein PET100, mitochondrial OS=Portunus trituberculatus OX=210409 GN=PET100 PE=4 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 9.820e-6
Identity = 21/46 (45.65%), Postives = 32/46 (69.57%), Query Frame = -2
Query:  238 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMYNEL 375
            MGGWKLE+ +M+ Y+SFPV  ++VFN  K+    T + R+++Y  L
Sbjct:    1 MGGWKLEIGKMAMYMSFPVMLFYVFNQPKYFEEWTVRMRRELYPPL 46          
BLAST of SMED30011746 vs. Planmine SMEST
Match: SMESG000036519.1 (SMESG000036519.1)

HSP 1 Score: 154.066 bits (388), Expect = 4.254e-49
Identity = 73/73 (100.00%), Postives = 73/73 (100.00%), Query Frame = -2
Query:  157 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMYNELGIDFYSNDIVPLEEALAQKSIFDKLVK 375
            MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMYNELGIDFYSNDIVPLEEALAQKSIFDKLVK
Sbjct:    1 MGGWKLEVARMSFYLSFPVACYFVFNSQKFITYCTNKYRQDMYNELGIDFYSNDIVPLEEALAQKSIFDKLVK 73          
The following BLAST results are available for this feature:
BLAST of SMED30011746 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 SMED30011746 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 SMED30011746 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 3
Match NameE-valueIdentityDescription
CG144839.890e-637.21gene:FBgn0034248 transcript:FBtr0345525[more]
CG144839.890e-637.21gene:FBgn0034248 transcript:FBtr0086902[more]
CG144839.890e-637.21gene:FBgn0034248 transcript:FBtr0329863[more]
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BLAST of SMED30011746 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 SMED30011746 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 SMED30011746 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 SMED30011746 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 SMED30011746 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A5K3ETX66.500e-637.66Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A5B7HAC59.820e-645.65Protein PET100, mitochondrial OS=Portunus trituber... [more]
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BLAST of SMED30011746 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 SMED30011746 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 SMED30011746 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 SMED30011746 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 SMED30011746 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 SMED30011746 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000036519.14.254e-49100.00SMESG000036519.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011746 ID=SMED30011746|Name=SMED30011746|organism=Schmidtea mediterranea sexual|type=transcript|length=565bp
TAATACCATTAAGTGTATTATTACCAAAACCAAATGCTTTAATCGTCGAA
AGTAAATTTAATCAATTAAGTTTAGCATCAATAAACCACATAACAAACTA
GATTTAATTATTACTATGACAACTAACAAAAAATAGTTTCAAAATAACAA
AGATTATTTTACTAATTTATCAAATATCGACTTTTGTGCAAGAGCTTCTT
CAAGTGGAACAATATCATTGGAGTAGAAATCTATTCCTAATTCATTATAC
ATATCCTGTCGATATTTATTAGTACAATAAGTTATGAATTTTTGAGAATT
AAAAACGAAATAACAAGCAACAGGAAAAGATAAGTAAAATGACATTCTAG
CAACTTCTAATTTCCAACCACCCATAATTAGTATTTCAAAAATATCAAAA
AAATTAGTAATATAATTTCAAATTAAATTTTATATTTATTTATAAGTTTA
AAAACTTTATGTTGATCTTAATTGCGTTCAATGGCTGCAATCATTTTCTT
GTCACATTGGTTTCTTTGACTTTTATTTCGATTTTGCGTGTTTAATAAAT
GTATTAACGTTTTCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR018625Pet100
Vocabulary: biological process
TermDefinition
GO:0033617mitochondrial respiratory chain complex IV assembly
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018625Protein Pet100PFAMPF09803Pet100coord: 1..59
e-value: 1.9E-14
score: 53.9
NoneNo IPR availableTMHMMTMhelixcoord: 10..27