SMED30023898

Overview
NameSMED30023898
Smed IDSMED30023898
Length (bp)504
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30023898 (SMED30023898) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023898 (SMED30023898) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30023898

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30023898SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000073751.1 SMESG000073596.1 SMESG000068623.1 SMESG000066691.1 SMESG000062442.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036051.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030069.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000012903.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002239.1 SMESG000080313.1 SMESG000069906.1 SMESG000066842.1 SMESG000050392.1 SMESG000033095.1 SMESG000017493.1 SMESG000004603.1 SMESG000004121.1 Contig42477newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023898SMESG000081995.1 SMESG000080328.1 SMESG000080048.1 SMESG000078665.1 SMESG000077025.1 SMESG000076395.1 SMESG000075858.1 SMESG000073751.1 SMESG000073596.1 SMESG000068623.1 SMESG000066691.1 SMESG000062442.1 SMESG000054975.1 SMESG000054276.1 SMESG000051957.1 SMESG000049162.1 SMESG000046165.1 SMESG000036051.1 SMESG000035648.1 SMESG000034762.1 SMESG000030928.1 SMESG000030069.1 SMESG000029599.1 SMESG000029355.1 SMESG000027993.1 SMESG000027217.1 SMESG000022058.1 SMESG000012961.1 SMESG000012903.1 SMESG000010709.1 SMESG000007675.1 SMESG000006952.1 SMESG000004166.1 SMESG000003706.1 SMESG000002239.1 SMESG000080313.1 SMESG000069906.1 SMESG000066842.1 SMESG000050392.1 SMESG000033095.1 SMESG000017493.1 SMESG000004603.1 SMESG000004121.1 Contig42477uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
whole organismSMED30023898SMESG000079687.1 SMESG000045335.1 SMESG000039707.1 SMESG000017814.1 SMESG000009171.1 Contig13588newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30023898SMESG000079687.1 SMESG000045335.1 SMESG000039707.1 SMESG000017814.1 SMESG000009171.1 Contig13588uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30023898 vs. Planmine SMEST
Match: SMESG000064381.1 (SMESG000064381.1)

HSP 1 Score: 173.711 bits (439), Expect = 1.466e-56
Identity = 82/101 (81.19%), Postives = 94/101 (93.07%), Query Frame = 2 
Query:  173 MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYIRLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQLP 475
            M+ L+++Q+ELDRARQ NAELLNQ+LQLTRE+QQ+KAT  DPKRTK LY RLTAAQKGWAEERQLN+SLRTQ+RGLEVALA CREGEAVTYPLIFAP+Q+P
Sbjct:    1 MASLRILQTELDRARQANAELLNQVLQLTREMQQIKATCLDPKRTKVLYQRLTAAQKGWAEERQLNRSLRTQVRGLEVALAVCREGEAVTYPLIFAPTQMP 101
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BLAST of SMED30023898 vs. Planmine SMEST
Match: SMESG000067481.1 (SMESG000067481.1)

HSP 1 Score: 177.178 bits (448), Expect = 6.008e-56
Identity = 83/101 (82.18%), Postives = 95/101 (94.06%), Query Frame = 2 
Query:  173 MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYIRLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQLP 475
            M+  +L+Q+ELD AR+TNA LL+QI+Q+TREVQQ+K+TWSDPK+TKALY+RLTAAQKGW EERQLNQSLRTQIRGLEVALA CREGEAVTYPLIFAPSQLP
Sbjct:    1 MTTTQLLQTELDHARRTNANLLDQIVQITREVQQIKSTWSDPKKTKALYLRLTAAQKGWVEERQLNQSLRTQIRGLEVALAVCREGEAVTYPLIFAPSQLP 101
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BLAST of SMED30023898 vs. Planmine SMEST
Match: SMESG000062652.1 (SMESG000062652.1)

HSP 1 Score: 170.629 bits (431), Expect = 4.966e-55
Identity = 83/109 (76.15%), Postives = 96/109 (88.07%), Query Frame = 2 
Query:  173 MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYIRLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQLPSQRVVDEA 499
            M+  +L+Q+EL  AR+ NA LL+QI+QLTRE QQ+K+TWSDPKRTKALY+RLTAAQKGWAEERQLNQSLRTQIRGLEVALAA REGEAVTYPLIFAPSQL  +  ++ A
Sbjct:    1 MTSTQLLQTELAHARRANANLLDQIVQLTRETQQIKSTWSDPKRTKALYLRLTAAQKGWAEERQLNQSLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDPINNA 109
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BLAST of SMED30023898 vs. Planmine SMEST
Match: SMESG000036810.1 (SMESG000036810.1)

HSP 1 Score: 173.711 bits (439), Expect = 6.377e-55
Identity = 82/101 (81.19%), Postives = 94/101 (93.07%), Query Frame = 2 
Query:  173 MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYIRLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQLP 475
            M+ L+++Q+ELDRARQ NAELLNQ+LQLTRE+QQ+KAT  DPKRTK LY RLTAAQKGWAEERQLN+SLRTQ+RGLEVALA CREGEAVTYPLIFAP+Q+P
Sbjct:    1 MASLRILQTELDRARQANAELLNQVLQLTREMQQIKATCLDPKRTKVLYQRLTAAQKGWAEERQLNRSLRTQVRGLEVALAVCREGEAVTYPLIFAPTQMP 101
[Close]
BLAST of SMED30023898 vs. Planmine SMEST
Match: SMESG000023001.1 (SMESG000023001.1)

HSP 1 Score: 167.548 bits (423), Expect = 5.754e-54
Identity = 79/101 (78.22%), Postives = 90/101 (89.11%), Query Frame = 2 
Query:  173 MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYIRLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQLP 475
            MS L+++Q+ELDRARQ N ELL QI+QLTRE+Q +KATW+D  +TK +Y RLTAAQKGW EERQLNQSLRTQIRGLEVALA CREGEAVTYPLIFAP+QLP
Sbjct:    1 MSSLRILQTELDRARQANMELLAQIIQLTREMQHMKATWTDHAKTKTIYHRLTAAQKGWEEERQLNQSLRTQIRGLEVALAVCREGEAVTYPLIFAPTQLP 101
The following BLAST results are available for this feature:
BLAST of SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 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 SMED30023898 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000064381.11.466e-5681.19SMESG000064381.1[more]
SMESG000067481.16.008e-5682.18SMESG000067481.1[more]
SMESG000062652.14.966e-5576.15SMESG000062652.1[more]
SMESG000036810.16.377e-5581.19SMESG000036810.1[more]
SMESG000023001.15.754e-5478.22SMESG000023001.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023898 ID=SMED30023898|Name=SMED30023898|organism=Schmidtea mediterranea sexual|type=transcript|length=504bp
TGGACAAAACCATAAATAACAATCTGCTTTAGTGATGTTGTCAATATAAT
AATTGCTATGAGTTGTTCGTCTTACTTTTATGAACAGATTTCCTTTCCAT
AACTATGTTTGCAACCATCAGAATTTCTCTCATTAAACTCATAAAGTTAA
TTTGAATGTTTTCTTTATAGCAATGTCGGTCCTAAAATTGATGCAAAGCG
AACTAGACCGCGCCAGGCAGACAAACGCGGAGCTACTCAATCAGATACTG
CAATTAACTCGCGAGGTGCAGCAGGTCAAAGCGACTTGGTCCGACCCCAA
AAGGACGAAGGCACTCTATATCCGACTCACTGCAGCTCAGAAGGGCTGGG
CGGAGGAGCGCCAGCTCAATCAGAGTCTTCGCACACAGATTAGGGGTTTA
GAAGTTGCCCTAGCAGCCTGTCGGGAAGGGGAAGCGGTAACGTATCCGCT
CATCTTCGCCCCTTCCCAACTGCCAAGCCAACGTGTCGTTGATGAAGCCA
CACC
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protein sequence of SMED30023898-orf-1

>SMED30023898-orf-1 ID=SMED30023898-orf-1|Name=SMED30023898-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp
MSVLKLMQSELDRARQTNAELLNQILQLTREVQQVKATWSDPKRTKALYI
RLTAAQKGWAEERQLNQSLRTQIRGLEVALAACREGEAVTYPLIFAPSQL
PSQRVVDEAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism