SMED30009466

Overview
NameSMED30009466
Smed IDSMED30009466
Length (bp)322
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 SMED30009466 (SMED30009466) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009466 (SMED30009466) 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 SMED30009466 (SMED30009466) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009466 (SMED30009466) 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



SMED30009466

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30009466SMESG000057261.1 Contig1882newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30009466SMESG000015244.1 SMESG000015241.1 SMESG000004848.1 SMESG000004822.1 SMESG000004820.1 SMESG000004806.1 Contig1882newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30009466SMESG000057261.1 SmedASXL_003644SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30009466SMESG000057261.1 dd_Smed_v4_2910_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009466SMESG000057261.1 dd_Smed_v4_2910_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009466SMESG000057261.1 dd_Smed_v4_2910_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30009466SMESG000057261.1 dd_Smed_v4_2910_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30009466SMESG000057261.1 dd_Smed_v6_2910_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009466 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001144:113692..117714 -1039
Homology
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BLAST of SMED30009466 vs. TrEMBL
Match: A0A4Z2CWI8 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_006948 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 2.921e-14
Identity = 37/71 (52.11%), Postives = 47/71 (66.20%), Query Frame = 2 
Query:   98 KRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSA---KRWFPVKELNYDDAIEV 301
            KRWFPVK   YGE +EV++  Y       K+WFPVKE  +GE +EVK+ S    KRW+PVKE +Y + IEV
Sbjct:   39 KRWFPVKEFHYGEPLEVRKKFY-------KRWFPVKEFHYGEPIEVKKRSNFVDKRWYPVKEFHYGEPIEV 102
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BLAST of SMED30009466 vs. TrEMBL
Match: Q5D8N2 (SJCHGC07290 protein OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 3.118e-14
Identity = 37/71 (52.11%), Postives = 47/71 (66.20%), Query Frame = 2 
Query:   98 KRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSA---KRWFPVKELNYDDAIEV 301
            KRWFPVK   YGE +EV++  Y       K+WFPVKE  +GE +EVK+ S    KRW+PVKE +Y + IEV
Sbjct:   39 KRWFPVKEFHYGEPLEVRKKFY-------KRWFPVKEFHYGEPIEVKKRSNFVDKRWYPVKEFHYGEPIEV 102
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BLAST of SMED30009466 vs. TrEMBL
Match: A0A5K4F205 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 6.444e-9
Identity = 33/71 (46.48%), Postives = 43/71 (60.56%), Query Frame = 2 
Query:   98 KRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSA---KRWFPVKELNYDDAIEV 301
            KRW+PVK   Y E +E+K    K     +K+WFPVKE  +   +EVK+      KRW PVKE +YD+ IEV
Sbjct:   49 KRWYPVKEFHYDEPLEIK----KRPLMFHKRWFPVKEFHYDGPLEVKKRPKFYDKRWSPVKEFHYDEPIEV 115
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BLAST of SMED30009466 vs. TrEMBL
Match: A0A4Z2CW62 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_006948 PE=4 SV=1)

HSP 1 Score: 55.0694 bits (131), Expect = 1.007e-7
Identity = 23/39 (58.97%), Postives = 30/39 (76.92%), Query Frame = 2 
Query:  185 KKWFPVKELDFGEAVEVKRNSAKRWFPVKELNYDDAIEV 301
            K+WFPVKE  +GE +EV++   KRWFPVKE +Y + IEV
Sbjct:   39 KRWFPVKEFHYGEPLEVRKKFYKRWFPVKEFHYGEPIEV 77

HSP 2 Score: 52.373 bits (124), Expect = 1.031e-6
Identity = 25/48 (52.08%), Postives = 32/48 (66.67%), Query Frame = 2 
Query:   98 KRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKR 241
            KRWFPVK   YGE +EV++  Y       K+WFPVKE  +GE +EVK+
Sbjct:   39 KRWFPVKEFHYGEPLEVRKKFY-------KRWFPVKEFHYGEPIEVKK 79
[Close]
BLAST of SMED30009466 vs. Planmine SMEST
Match: SMESG000057261.1 (SMESG000057261.1)

HSP 1 Score: 203.371 bits (516), Expect = 1.290e-69
Identity = 100/100 (100.00%), Postives = 100/100 (100.00%), Query Frame = 2 
Query:    2 MSFIRFSIAVPVLILAWNLILTFQRSDGFETKKRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSAKRWFPVKELNYDDAIEV 301
            MSFIRFSIAVPVLILAWNLILTFQRSDGFETKKRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSAKRWFPVKELNYDDAIEV
Sbjct:    1 MSFIRFSIAVPVLILAWNLILTFQRSDGFETKKRWFPVKTLDYGEAVEVKRPHYKLESRKNKKWFPVKELDFGEAVEVKRNSAKRWFPVKELNYDDAIEV 100
The following BLAST results are available for this feature:
BLAST of SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A4Z2CWI82.921e-1452.11Uncharacterized protein OS=Schistosoma japonicum O... [more]
Q5D8N23.118e-1452.11SJCHGC07290 protein OS=Schistosoma japonicum OX=61... [more]
A0A5K4F2056.444e-946.48Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A4Z2CW621.007e-758.97Uncharacterized protein OS=Schistosoma japonicum O... [more]
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BLAST of SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 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 SMED30009466 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000057261.11.290e-69100.00SMESG000057261.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009466 ID=SMED30009466|Name=SMED30009466|organism=Schmidtea mediterranea sexual|type=transcript|length=322bp
AATGTCTTTTATTAGGTTTTCTATAGCTGTGCCAGTTCTAATTCTCGCGT
GGAATTTGATTTTAACATTTCAAAGATCAGATGGATTTGAAACCAAAAAA
AGATGGTTTCCAGTGAAAACATTGGATTATGGTGAAGCCGTTGAGGTGAA
ACGCCCTCATTATAAGTTGGAATCTAGAAAAAATAAGAAATGGTTCCCAG
TTAAGGAGTTAGATTTCGGAGAAGCCGTTGAAGTAAAGAGGAATTCTGCA
AAACGGTGGTTCCCAGTAAAGGAGCTAAATTATGATGACGCCATTGAAGT
TTAGGAATTGAATCACATAGAT
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protein sequence of SMED30009466-orf-1

>SMED30009466-orf-1 ID=SMED30009466-orf-1|Name=SMED30009466-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MSFIRFSIAVPVLILAWNLILTFQRSDGFETKKRWFPVKTLDYGEAVEVK
RPHYKLESRKNKKWFPVKELDFGEAVEVKRNSAKRWFPVKELNYDDAIEV
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000418head
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
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..28
score: 0.743
NoneNo IPR availableTMHMMTMhelixcoord: 4..23