SMED30012778

Overview
NameSMED30012778
Smed IDSMED30012778
Length (bp)1155
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 SMED30012778 (SMED30012778) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012778 (SMED30012778) 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 SMED30012778 (SMED30012778) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012778 (SMED30012778) 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



SMED30012778

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30012778 dd_Smed_v4_17023_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
Alignments
SMED30012778 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000185:69444..71346 -5598
Homology
[Close]
BLAST of SMED30012778 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 107.457 bits (267), Expect = 2.287e-38
Identity = 51/123 (41.46%), Postives = 82/123 (66.67%), Query Frame = 3 
Query:  750 PVCSIKCKPGRNPAREARHKAEYTLAKLEELQCKTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLIRTS-------------AYTSQRPREDSN 1079
            P  +IKC+PG+NPAREAR +AE++  K+E+++ K   + ++AR+ L+++N DIA+  IP TDG+   YG+S+EL+DP L +M AP  +V+P R+I+++              YTS+ PR + N
Sbjct:  719 PSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGFPPEYGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQTGDHMYTSRHPRWNFN 841

HSP 2 Score: 70.8626 bits (172), Expect = 2.287e-38
Identity = 31/56 (55.36%), Postives = 39/56 (69.64%), Query Frame = 2 
Query:  590 GSWNDNSRNTIRFPVRAAARCNQAIWDSGYTVSSAGGSSWPNLSTSQNDEIELPCV 757
            GSWNDNSR T+R P  +AAR  Q +WD+GY +S  G SSWP  S  Q +E+ELP +
Sbjct:  666 GSWNDNSRVTLRIPSASAARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSI 721
[Close]
BLAST of SMED30012778 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 107.457 bits (267), Expect = 2.464e-38
Identity = 51/123 (41.46%), Postives = 82/123 (66.67%), Query Frame = 3 
Query:  750 PVCSIKCKPGRNPAREARHKAEYTLAKLEELQCKTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLIRTS-------------AYTSQRPREDSN 1079
            P  +IKC+PG+NPAREAR +AE++  K+E+++ K   + ++AR+ L+++N DIA+  IP TDG+   YG+S+EL+DP L +M AP  +V+P R+I+++              YTS+ PR + N
Sbjct:  718 PSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGFPPEYGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQTGDHMYTSRHPRWNFN 840

HSP 2 Score: 70.8626 bits (172), Expect = 2.464e-38
Identity = 31/56 (55.36%), Postives = 39/56 (69.64%), Query Frame = 2 
Query:  590 GSWNDNSRNTIRFPVRAAARCNQAIWDSGYTVSSAGGSSWPNLSTSQNDEIELPCV 757
            GSWNDNSR T+R P  +AAR  Q +WD+GY +S  G SSWP  S  Q +E+ELP +
Sbjct:  665 GSWNDNSRVTLRIPSASAARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSI 720
[Close]
BLAST of SMED30012778 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 108.612 bits (270), Expect = 2.484e-38
Identity = 52/135 (38.52%), Postives = 82/135 (60.74%), Query Frame = 3 
Query:  750 PVCSIKCKPGRNPAREARHKAEYTLAKLEELQCKTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLIRTS-------------AYTSQRPREDSNFRYYNNQRRYGH 1115
            P  +IK +PG NPAREAR +A+Y   K+EEL+ K   + + AR+ L+++N DIA+  IP TDG+   YG+S+EL+DP L +M AP  +V+P +L++++              Y S+ P+ +S      ++R  GH
Sbjct: 1697 PSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTLRNQLGSHQTGDHTYASRHPQWNSKLNNRRSERFNGH 1831

HSP 2 Score: 69.707 bits (169), Expect = 2.484e-38
Identity = 30/56 (53.57%), Postives = 39/56 (69.64%), Query Frame = 2 
Query:  590 GSWNDNSRNTIRFPVRAAARCNQAIWDSGYTVSSAGGSSWPNLSTSQNDEIELPCV 757
            GSW+DNSR T+  P  +AAR  Q +WD+GY +S+ G SSWP  S  Q +EIELP +
Sbjct: 1644 GSWSDNSRVTLEIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSI 1699
[Close]
BLAST of SMED30012778 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 107.071 bits (266), Expect = 1.067e-37
Identity = 48/113 (42.48%), Postives = 75/113 (66.37%), Query Frame = 3 
Query:  750 PVCSIKCKPGRNPAREARHKAEYTLAKLEELQCKTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLIRTSAYTSQRPREDSNFRY 1088
            P  +IK +PG NPAREAR +AEY   K+EEL+ K   + ++AR+ L+++N DIA+  IP TDG+   YG+S+EL+DP L +M AP  +V+P +L++++       R+  +  Y
Sbjct: 1187 PSIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTY 1299

HSP 2 Score: 68.9366 bits (167), Expect = 1.067e-37
Identity = 29/56 (51.79%), Postives = 40/56 (71.43%), Query Frame = 2 
Query:  590 GSWNDNSRNTIRFPVRAAARCNQAIWDSGYTVSSAGGSSWPNLSTSQNDEIELPCV 757
            G+W+DNSR T++ P  +AAR  Q +WD+GY +S+ G SSWP  S  Q +EIELP +
Sbjct: 1134 GNWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSI 1189
[Close]
BLAST of SMED30012778 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 105.916 bits (263), Expect = 3.545e-37
Identity = 54/136 (39.71%), Postives = 82/136 (60.29%), Query Frame = 3 
Query:  747 CPVCSIKCKPGRNPAREARHKAEYTLAKLEELQCKTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLIRTS-------------AYTSQRPREDSNFRYYNNQRRYGH 1115
             P  +IK +PG NPAREAR +AEY   K EEL+ K   + ++AR+ L+++N DIA+  IP TDG+   YG+S+EL+DP L +M AP  +V+P +L+R++              Y S+ P+ +S      ++R  GH
Sbjct:  139 LPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQTGDHTYASRHPQWNSKHNNLRSERFNGH 274

HSP 2 Score: 68.1662 bits (165), Expect = 3.545e-37
Identity = 30/56 (53.57%), Postives = 40/56 (71.43%), Query Frame = 2 
Query:  590 GSWNDNSRNTIRFPVRAAARCNQAIWDSGYTVSSAGGSSWPNLSTSQNDEIELPCV 757
            GSW+DNSR T++ P  +AAR  Q +WD+GY +S+ G SSWP  S  Q +E+ELP V
Sbjct:   87 GSWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSV 142

HSP 3 Score: 65.855 bits (159), Expect = 7.183e-12
Identity = 32/55 (58.18%), Postives = 40/55 (72.73%), Query Frame = 3 
Query:  870 MARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEMEAPIHVVVPRRLI 1034
            MARR L RINA IA+ +IP TDGYA  YG+S+EL DPA   M+AP ++V+P  L 
Sbjct:    1 MARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDPA--RMKAPTNIVLPVNLF 53
The following BLAST results are available for this feature:
BLAST of SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 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 SMED30012778 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035366.12.287e-3841.46SMESG000035366.1[more]
SMESG000035366.12.464e-3841.46SMESG000035366.1[more]
SMESG000057533.12.484e-3838.52SMESG000057533.1[more]
SMESG000044971.11.067e-3742.48SMESG000044971.1[more]
SMESG000004883.13.545e-3739.71SMESG000004883.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012778 ID=SMED30012778|Name=SMED30012778|organism=Schmidtea mediterranea sexual|type=transcript|length=1155bp
GCCCTGTGGACCATAATTGAGCAAACTAGTCGCGATCACGTGATCCGAAT
TACTGAGTTCCATGATACTGTTCACTTGATTGAAAATTCTCGCACAAACT
AATAAAACCGGATCAATCGATTTGAATATACCAATTGGCACAGCACACTA
AATGTCACTTCTAGAGATGCATAAGCACACGTTTTATCTGAACACCATCG
AGGGTGTCGTTTGTAACAATCAGTGTGCTAAAGTGACTTACTGAATTAAT
GAAAATAGATCCATCTGCAAAAAATCCAGAAAATAAGAAATACTAAATTA
ATCTATGGAAGAAACAAAAATATCGATCGGAATTTATTAAAAGTCACCGG
CAGATATCGAATTCCTTCACGACTGTTATAAATACACGTGCCAACGATGG
AAGAGTGAATAGTTAACTGAAATTATGCCAACCAACTAAGGAGAATCAAC
AAATAAAGGAAAATCCTTGACCTCAAGGACAAATAGTGGTCGCGTTGAAC
AAGCATATATCGGAGACGACAAGGGAACTAATCCGAATTCTGTAACGAAT
GATGCTAGACAATTTGCGGCAGATATACCACCCATGGACGGATCCTGGAA
TGATAATTCTAGAAACACGATCAGATTTCCAGTCAGAGCAGCTGCCCGGT
GCAATCAAGCCATATGGGATTCTGGATATACCGTGTCATCCGCAGGAGGA
TCCAGCTGGCCAAACCTTTCAACGAGTCAAAACGACGAGATCGAACTGCC
CTGTGTGTTCAATCAAATGCAAACCAGGACGAAACCCAGCGCGAGAAGCT
CGGCATAAGGCTGAGTATACTCTGGCCAAGTTGGAAGAGTTGCAATGCAA
GACACTGTGGCAGATAATCATGGCGCGACGCCACCTCAGTAGAATCAACG
CAGATATCGCAGCAGCTCAAATACCCAGAACCGACGGGTACGCTCTTAGC
TATGGGATCTCTTACGAATTAAATGATCCAGCCTTGGAAGAAATGGAGGC
GCCAATACACGTAGTGGTACCAAGACGGCTTATTCGAACATCAGCTTATA
CGAGTCAACGGCCAAGAGAAGATTCAAATTTTCGGTACTATAATAACCAG
AGAAGGTATGGACATCCATGAACCAACGTTGGAGACAATGTAACAAATTC
TGTTG
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protein sequence of SMED30012778-orf-1

>SMED30012778-orf-1 ID=SMED30012778-orf-1|Name=SMED30012778-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=191bp
MMLDNLRQIYHPWTDPGMIILETRSDFQSEQLPGAIKPYGILDIPCHPQE
DPAGQTFQRVKTTRSNCPVCSIKCKPGRNPAREARHKAEYTLAKLEELQC
KTLWQIIMARRHLSRINADIAAAQIPRTDGYALSYGISYELNDPALEEME
APIHVVVPRRLIRTSAYTSQRPREDSNFRYYNNQRRYGHP*
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