SMED30020950

Overview
NameSMED30020950
Smed IDSMED30020950
Length (bp)412
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 SMED30020950 (SMED30020950) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020950 (SMED30020950) 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 SMED30020950 (SMED30020950) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020950 (SMED30020950) 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




SMED30020950

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30020950SMESG000055070.1 dd_Smed_v4_6915_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020950SMESG000055070.1 Contig33876uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020950SMESG000055070.1 Contig33876newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
musculature systemSMED30020950SMESG000055070.1 dd_Smed_v6_6915_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle progenitor cellSMED30020950SMESG000055070.1 dd_Smed_v6_6915_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30020950SMESG000055070.1 dd_Smed_v6_6915_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30020950SMESG000055070.1 dd_Smed_v4_6915_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
SMED30020950 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001574:1485..2524 -1993
Homology
BLAST of SMED30020950 vs. Planmine SMEST
Match: SMESG000055070.1 (SMESG000055070.1)

HSP 1 Score: 277.715 bits (709), Expect = 2.793e-87
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 1
Query:    1 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL 411
            SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVV GL
Sbjct: 3291 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVAGL 3427          

HSP 2 Score: 58.151 bits (139), Expect = 1.269e-10
Identity = 27/78 (34.62%), Postives = 46/78 (58.97%), Query Frame = 1
Query:  130 EIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPV 363
            EIDCL+ GG+PP    W+  K+S+  +L + +    + V++K+ +IL+++  N+ +  N  L C VKD+ G   S  V
Sbjct: 3011 EIDCLYSGGKPPLVADWFLEKNSEMRKLPRGDSVKKYKVFEKRSDILSIRTENITQVMNFKLKCFVKDSAGTEFSDSV 3088          
BLAST of SMED30020950 vs. Planmine SMEST
Match: SMESG000055070.1 (SMESG000055070.1)

HSP 1 Score: 277.715 bits (709), Expect = 2.847e-87
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 1
Query:    1 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL 411
            SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVV GL
Sbjct: 3291 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVAGL 3427          

HSP 2 Score: 58.151 bits (139), Expect = 1.268e-10
Identity = 27/78 (34.62%), Postives = 46/78 (58.97%), Query Frame = 1
Query:  130 EIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPV 363
            EIDCL+ GG+PP    W+  K+S+  +L + +    + V++K+ +IL+++  N+ +  N  L C VKD+ G   S  V
Sbjct: 3011 EIDCLYSGGKPPLVADWFLEKNSEMRKLPRGDSVKKYKVFEKRSDILSIRTENITQVMNFKLKCFVKDSAGTEFSDSV 3088          
BLAST of SMED30020950 vs. Planmine SMEST
Match: SMESG000055070.1 (SMESG000055070.1)

HSP 1 Score: 277.715 bits (709), Expect = 2.903e-87
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 1
Query:    1 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL 411
            SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVV GL
Sbjct: 3251 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVAGL 3387          

HSP 2 Score: 58.151 bits (139), Expect = 1.256e-10
Identity = 27/78 (34.62%), Postives = 46/78 (58.97%), Query Frame = 1
Query:  130 EIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPV 363
            EIDCL+ GG+PP    W+  K+S+  +L + +    + V++K+ +IL+++  N+ +  N  L C VKD+ G   S  V
Sbjct: 2971 EIDCLYSGGKPPLVADWFLEKNSEMRKLPRGDSVKKYKVFEKRSDILSIRTENITQVMNFKLKCFVKDSAGTEFSDSV 3048          
BLAST of SMED30020950 vs. Planmine SMEST
Match: SMESG000055070.1 (SMESG000055070.1)

HSP 1 Score: 277.715 bits (709), Expect = 2.932e-87
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 1
Query:    1 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL 411
            SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVV GL
Sbjct: 3291 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVAGL 3427          

HSP 2 Score: 58.151 bits (139), Expect = 1.281e-10
Identity = 27/78 (34.62%), Postives = 46/78 (58.97%), Query Frame = 1
Query:  130 EIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPV 363
            EIDCL+ GG+PP    W+  K+S+  +L + +    + V++K+ +IL+++  N+ +  N  L C VKD+ G   S  V
Sbjct: 3011 EIDCLYSGGKPPLVADWFLEKNSEMRKLPRGDSVKKYKVFEKRSDILSIRTENITQVMNFKLKCFVKDSAGTEFSDSV 3088          
BLAST of SMED30020950 vs. Planmine SMEST
Match: SMESG000055070.1 (SMESG000055070.1)

HSP 1 Score: 277.715 bits (709), Expect = 2.932e-87
Identity = 136/137 (99.27%), Postives = 136/137 (99.27%), Query Frame = 1
Query:    1 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL 411
            SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVV GL
Sbjct: 3291 SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVAGL 3427          

HSP 2 Score: 58.151 bits (139), Expect = 1.281e-10
Identity = 27/78 (34.62%), Postives = 46/78 (58.97%), Query Frame = 1
Query:  130 EIDCLHFGGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKNSNMTLNCVVKDANGVMISSPV 363
            EIDCL+ GG+PP    W+  K+S+  +L + +    + V++K+ +IL+++  N+ +  N  L C VKD+ G   S  V
Sbjct: 3011 EIDCLYSGGKPPLVADWFLEKNSEMRKLPRGDSVKKYKVFEKRSDILSIRTENITQVMNFKLKCFVKDSAGTEFSDSV 3088          
The following BLAST results are available for this feature:
BLAST of SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 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 SMED30020950 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000055070.12.793e-8799.27SMESG000055070.1[more]
SMESG000055070.12.847e-8799.27SMESG000055070.1[more]
SMESG000055070.12.903e-8799.27SMESG000055070.1[more]
SMESG000055070.12.932e-8799.27SMESG000055070.1[more]
SMESG000055070.12.932e-8799.27SMESG000055070.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020950 ID=SMED30020950|Name=SMED30020950|organism=Schmidtea mediterranea sexual|type=transcript|length=412bp
TCAATCACTTTGGATACCAAAATTAAACCAGTATTCAAACCATTAATTGT
TTCGGTATATTCGAAAGATGTGAATTTTACTGTTAAAGATAAGAGAAATA
CAGCTATTTTACCCGAGTACAGAGTGATAGAAATAGATTGTTTGCATTTC
GGGGGCCAGCCACCAACTGATGTCACTTGGTATCAAATAAAGGATTCTCA
GGAAGTGGAATTGTTAAAAAGTGAAATCAAGGACAACTTCAATGTTTACC
AGAAACAACCTAACATTTTAACTGTGAAAATATTGAATATGAAAAAGAAT
TCAAACATGACTTTGAACTGTGTTGTTAAAGATGCTAATGGTGTTATGAT
ATCCAGTCCAGTGTTCTTAACTCAATCTCCATCCGGAGTGAGATTTGTGG
TTACCGGTCTTG
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protein sequence of SMED30020950-orf-1

>SMED30020950-orf-1 ID=SMED30020950-orf-1|Name=SMED30020950-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp
SITLDTKIKPVFKPLIVSVYSKDVNFTVKDKRNTAILPEYRVIEIDCLHF
GGQPPTDVTWYQIKDSQEVELLKSEIKDNFNVYQKQPNILTVKILNMKKN
SNMTLNCVVKDANGVMISSPVFLTQSPSGVRFVVTGL
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000019muscle progenitor cell
PLANA:0000101muscle cell
PLANA:0000428musculature system
PLANA:0000478pharynx musculature
Vocabulary: INTERPRO
TermDefinition
IPR013783Ig-like_fold
IPR007110Ig-like_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding