SMED30026690

Overview
NameSMED30026690
Smed IDSMED30026690
Length (bp)600
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 SMED30026690 (SMED30026690) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026690 (SMED30026690) 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 SMED30026690 (SMED30026690) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026690 (SMED30026690) 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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Alignments
SMED30026690 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.036273:302..898 -2284
v31.030974:3400..3966 +2255
v31.004561:16090..16774 -2212
v31.004601:57879..58579 +1980
v31.013385:11612..12237 -1924
v31.036313:2496..3183 +1758
v31.012567:4110..4704 -1348
v31.012567:4150..4706 -844
Homology
BLAST of SMED30026690 vs. Planmine SMEST
Match: SMESG000048922.1 (SMESG000048922.1)

HSP 1 Score: 137.502 bits (345), Expect = 2.601e-37
Identity = 95/96 (98.96%), Postives = 95/96 (98.96%), Query Frame = -3
Query:  209 PRYCISSLQHNESCHEEMKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHLXXXXXXXXXXXXXXXXXNVDILNILQNKKTSNKKNKRPAA 496
            PRYCISSLQHNESCHEEMKKYYRHRFNGI FFICAICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNVDILNILQNKKTSNKKNKRPAA
Sbjct:  938 PRYCISSLQHNESCHEEMKKYYRHRFNGIKFFICAICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNVDILNILQNKKTSNKKNKRPAA 1033          
BLAST of SMED30026690 vs. Planmine SMEST
Match: SMESG000048922.1 (SMESG000048922.1)

HSP 1 Score: 137.502 bits (345), Expect = 2.759e-37
Identity = 95/96 (98.96%), Postives = 95/96 (98.96%), Query Frame = -3
Query:  209 PRYCISSLQHNESCHEEMKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHLXXXXXXXXXXXXXXXXXNVDILNILQNKKTSNKKNKRPAA 496
            PRYCISSLQHNESCHEEMKKYYRHRFNGI FFICAICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNVDILNILQNKKTSNKKNKRPAA
Sbjct:  980 PRYCISSLQHNESCHEEMKKYYRHRFNGIKFFICAICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNVDILNILQNKKTSNKKNKRPAA 1075          
BLAST of SMED30026690 vs. Planmine SMEST
Match: SMESG000076042.1 (SMESG000076042.1)

HSP 1 Score: 134.035 bits (336), Expect = 4.248e-36
Identity = 93/96 (96.88%), Postives = 94/96 (97.92%), Query Frame = -3
Query:  209 PRYCISSLQHNESCHEEMKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHLXXXXXXXXXXXXXXXXXNVDILNILQNKKTSNKKNKRPAA 496
            PRYCISSLQHNESCHEEMKKYYRHRFNGI FFIC ICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNV+ILNILQNKKTSNKKNKRPAA
Sbjct: 1110 PRYCISSLQHNESCHEEMKKYYRHRFNGIKFFICVICKTSQNIKYKEFYREHGVHLNSFKSSKINMFKKINKNNVNILNILQNKKTSNKKNKRPAA 1205          
BLAST of SMED30026690 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 85.1149 bits (209), Expect = 3.808e-19
Identity = 55/96 (57.29%), Postives = 67/96 (69.79%), Query Frame = -3
Query:  212 PRYCISSLQHNESCHEEMKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHLXXXXXXXXXXXXXXXXXNVDILNILQN-KKTSNKKNKRPA 496
            P+YC+ S  H E CHE+MK+YY HRFN I FFIC +CKTSQ+IKYK FY  H  HL+SFK  K  +F+  NKNNV+I+N + N   T   KNK PA
Sbjct:  717 PKYCMISKNHGEICHEKMKQYYVHRFNCIRFFICPVCKTSQSIKYKAFYNIHKDHLDSFKIIKKELFRISNKNNVNIMNTINNIHPTKITKNKIPA 812          
BLAST of SMED30026690 vs. Planmine SMEST
Match: SMESG000047874.1 (SMESG000047874.1)

HSP 1 Score: 75.485 bits (184), Expect = 9.188e-16
Identity = 31/56 (55.36%), Postives = 41/56 (73.21%), Query Frame = -3
Query:  329 PRYCISSLQHNESCHEEMKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHL 496
            P+YCISS  H+  CH EMK+YY  +F GI FFIC  C+T+Q++KY  FY++H  HL
Sbjct: 1073 PKYCISSACHSLECHAEMKRYYGQKFYGIKFFICPKCETAQDVKYLVFYKDHSSHL 1128          
The following BLAST results are available for this feature:
BLAST of SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 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 SMED30026690 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000048922.12.601e-3798.96SMESG000048922.1[more]
SMESG000048922.12.759e-3798.96SMESG000048922.1[more]
SMESG000076042.14.248e-3696.88SMESG000076042.1[more]
SMESG000057533.13.808e-1957.29SMESG000057533.1[more]
SMESG000047874.19.188e-1655.36SMESG000047874.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026690 ID=SMED30026690|Name=SMED30026690|organism=Schmidtea mediterranea sexual|type=transcript|length=600bp
AAAGACCATGACTCATTCAAGGTCGTTGGGTGACTCATCACACTTTTCAA
GGTCACTTAAACAAAGACCATGATTCATTCAAGGTCATTGGATGACTTAT
AATATTTTCATTATTTTCAATACTTACATTATTTATAATATTAGAGTCAT
CAATGATTTCGATGACTTCTTTTTTAATTATTTTATTTGGGATATTAATT
TTAATAGGTGCAGCAGGTCTTTTATTCTTTTTATTTGATGTTTTTTTATT
TTGTAGTATATTCAAAATATCGACGTTATTTTTATTAATTTTCTTAAACA
TATTTATTTTACTCGACTTGAAAGAATTTAAATGAACCCCATGTTCCCTA
TAAAATTCTTTATATTTAATGTTCTGGGATGTTTTGCATATGGCGCAGAT
AAAAAAGTTGATGCCATTAAATCTATGGCGGTAATATTTTTTCATTTCTT
CATGGCAACTTTCATTATGTTGCAATGATGAGATGCAATATCTTGGATAA
AAAAGTGCCTAATAAAAATATTAAATTAAAAACCTATATAAAGTAACTAT
GATATAAAATATCTAATAATTCTAACAAATAAAGTAACTAATAATATTTG
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protein sequence of SMED30026690-orf-1

>SMED30026690-orf-1 ID=SMED30026690-orf-1|Name=SMED30026690-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=131bp
MKKYYRHRFNGINFFICAICKTSQNIKYKEFYREHGVHLNSFKSSKINMF
KKINKNNVDILNILQNKKTSNKKNKRPAAPIKINIPNKIIKKEVIEIIDD
SNIINNVSIENNENIISHPMTLNESWSLFK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte