SMED30027072

Overview
NameSMED30027072
Smed IDSMED30027072
Length (bp)1086
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 SMED30027072 (SMED30027072) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027072 (SMED30027072) 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.
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



SMED30027072

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testisSMED30027072SMESG000067157.1 Contig488_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
early male germ cellSMED30027072SMESG000067157.1 Contig488_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism asexual adult cDNA to DNA expression microarray evidence
testis primordiumSMED30027072SMESG000067157.1 Contig488_SE3GPL10652PMID:20844018
Wang et al., 2010		whole organism juvenile cDNA to DNA expression microarray evidence
neoblastSMED30027072SMESG000067157.1 SMED_07083_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30027072SMESG000067157.1 SMED_07083_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30027072 vs. Planmine SMEST
Match: SMESG000067157.1 (SMESG000067157.1)

HSP 1 Score: 299.671 bits (766), Expect = 7.593e-103
Identity = 143/143 (100.00%), Postives = 143/143 (100.00%), Query Frame = 2 
Query:  584 MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD 1012
            MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD
Sbjct:    1 MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD 143

HSP 2 Score: 299.671 bits (766), Expect = 7.593e-103
Identity = 143/143 (100.00%), Postives = 143/143 (100.00%), Query Frame = -3 
Query:   68 MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD 496
            MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD
Sbjct:    1 MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYD 143
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BLAST of SMED30027072 vs. Planmine SMEST
Match: SMESG000076569.1 (SMESG000076569.1)

HSP 1 Score: 116.316 bits (290), Expect = 7.498e-31
Identity = 59/125 (47.20%), Postives = 83/125 (66.40%), Query Frame = 2 
Query:  590 NNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGD--ENN-----KGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYS 943
            N +VTYHSFLT++     + F +   + LL NIERSANC+I+TRP+V  D  EN+      GYW+TEI+YHQLYGKH++A+RMID  +  +++ +  S +R  +KT  GF +IED EI   +  S
Sbjct:   10 NKRVTYHSFLTTQHLVRDSLFSNPKFDNLLTNIERSANCIIRTRPLVQSDIKENDTNYRCSGYWITEIYYHQLYGKHEIAMRMIDAFMKDMERINNYSQHRVALKTTTGFFKIEDREILDKMDNS 134

HSP 2 Score: 116.316 bits (290), Expect = 7.498e-31
Identity = 59/125 (47.20%), Postives = 83/125 (66.40%), Query Frame = -3 
Query:  137 NNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVAGD--ENN-----KGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTLRGFHQIEDEEIAKSLSYS 490
            N +VTYHSFLT++     + F +   + LL NIERSANC+I+TRP+V  D  EN+      GYW+TEI+YHQLYGKH++A+RMID  +  +++ +  S +R  +KT  GF +IED EI   +  S
Sbjct:   10 NKRVTYHSFLTTQHLVRDSLFSNPKFDNLLTNIERSANCIIRTRPLVQSDIKENDTNYRCSGYWITEIYYHQLYGKHEIAMRMIDAFMKDMERINNYSQHRVALKTTTGFFKIEDREILDKMDNS 134
[Close]
BLAST of SMED30027072 vs. Planmine SMEST
Match: SMESG000051444.1 (SMESG000051444.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.568e-7
Identity = 32/107 (29.91%), Postives = 56/107 (52.34%), Query Frame = 2 
Query:  596 KVTYHSFLTSKGNE-DLNPFVDYSLNPLLRNIERSANCLIKTR--------PMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTL 889
            ++ YHSFL  +  +   N F D S   +++ IE++  C IKT         P+ +   +  GY +TEI Y++ + +H++A++MID +       +  S NR   KT+
Sbjct:    7 RIIYHSFLILQNKKFHSNLFTDKSFERVIQLIEKTCRCRIKTSLLKINLKFPLNSRITDLSGYLITEIFYYEPFNQHNIAMKMIDHLFRVSAFETHYSCNRLAYKTI 113

HSP 2 Score: 52.7582 bits (125), Expect = 1.568e-7
Identity = 32/107 (29.91%), Postives = 56/107 (52.34%), Query Frame = -3 
Query:  191 KVTYHSFLTSKGNE-DLNPFVDYSLNPLLRNIERSANCLIKTR--------PMVAGDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVKTL 484
            ++ YHSFL  +  +   N F D S   +++ IE++  C IKT         P+ +   +  GY +TEI Y++ + +H++A++MID +       +  S NR   KT+
Sbjct:    7 RIIYHSFLILQNKKFHSNLFTDKSFERVIQLIEKTCRCRIKTSLLKINLKFPLNSRITDLSGYLITEIFYYEPFNQHNIAMKMIDHLFRVSAFETHYSCNRLAYKTI 113
The following BLAST results are available for this feature:
BLAST of SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 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 SMED30027072 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000067157.17.593e-103100.00SMESG000067157.1[more]
SMESG000076569.17.498e-3147.20SMESG000076569.1[more]
SMESG000051444.11.568e-729.91SMESG000051444.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027072 ID=SMED30027072|Name=SMED30027072|organism=Schmidtea mediterranea sexual|type=transcript|length=1086bp
CTGGAATTTAAACTATTTATTATTTAAAACTTTGAGAATGTGACATTTAA
TGTTGACTTTGAGATTGATCATAGCTTTCATTCTTTTGGATTCGATACTT
TTCAAGGAGAGAACGCCGAAATCCGTGCGGGTAAACCGAATAACTTAGAC
TTTTAGCTATTTCTTCATCTTCAATTTGATGGAATCCTCTTAGTGTTTTG
ACAGGTGTTCGGTTAATACTAATTTTTGAAGTCTTCTTCAGCGTATCCAA
AACCCCATCTATCATACGTATTGCCAAATCATGTTTGCCATAGAGTTGGT
GATAATGAATTTCTGTCACCCAATACCCTTTATTGTTCTCGTCTCCAGCT
ACCATGGGCCTGGTCTTGATAAGGCAATTGGCACTCCGTTCAATATTTCG
TAATAATGGGTTCAAGGAATAATCAACAAATGGATTTAGGTCTTCGTTTC
CTTTCGAGGTAAGGAAAGAGTGATAGGTAACTTTGTTGTTACGCATATAT
ATTTGGTTTATAAATTCAATATATCTATGTAATTACTTTTGAAAAATAAT
TAAATATTTAATGAATCAATAAACCAAATATATATGCGTAACAACAAAGT
TACCTATCACTCTTTCCTTACCTCGAAAGGAAACGAAGACCTAAATCCAT
TTGTTGATTATTCCTTGAACCCATTATTACGAAATATTGAACGGAGTGCC
AATTGCCTTATCAAGACCAGGCCCATGGTAGCTGGAGACGAGAACAATAA
AGGGTATTGGGTGACAGAAATTCATTATCACCAACTCTATGGCAAACATG
ATTTGGCAATACGTATGATAGATGGGGTTTTGGATACGCTGAAGAAGACT
TCAAAAATTAGTATTAACCGAACACCTGTCAAAACACTAAGAGGATTCCA
TCAAATTGAAGATGAAGAAATAGCTAAAAGTCTAAGTTATTCGGTTTACC
CGCACGGATTTCGGCGTTCTCTCCTTGAAAAGTATCGAATCCAAAAGAAT
GAAAGCTATGATCAATCTCAAAGTCAACATTAAATGTCACATTCTCAAAG
TTTTAAATAATAAATAGTTTAAATTCCAAAAAAAAA
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protein sequence of SMED30027072-orf-1

>SMED30027072-orf-1 ID=SMED30027072-orf-1|Name=SMED30027072-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVA
GDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVK
TLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYDQSQSQH*
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protein sequence of SMED30027072-orf-2

>SMED30027072-orf-2 ID=SMED30027072-orf-2|Name=SMED30027072-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=150bp
MRNNKVTYHSFLTSKGNEDLNPFVDYSLNPLLRNIERSANCLIKTRPMVA
GDENNKGYWVTEIHYHQLYGKHDLAIRMIDGVLDTLKKTSKISINRTPVK
TLRGFHQIEDEEIAKSLSYSVYPHGFRRSLLEKYRIQKNESYDQSQSQH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000429neoblast
PLANA:0002030early male germ cell
PLANA:0003304testis primordium