SMED30023357

Overview
NameSMED30023357
Smed IDSMED30023357
Length (bp)799
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 SMED30023357 (SMED30023357) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023357 (SMED30023357) 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 SMED30023357 (SMED30023357) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023357 (SMED30023357) 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



SMED30023357

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30023357h1SMcG0000164 Contig44957newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023357h1SMcG0000164 Contig44957uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023357h1SMcG0003326 Contig12809uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023357h1SMcG0003326 Contig12809newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023357h1SMcG0013084 Contig17705newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023357h1SMcG0013084 Contig17705uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
reproductive organSMED30023357h1SMcG0003819 Contig36569uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023357h1SMcG0003819 Contig36569newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30023357h1SMcG0013084 Contig16275newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30023357h1SMcG0013084 Contig16275uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30023357h1SMcG0013084 Contig16275newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30023357h1SMcG0013084 Contig16275uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023357h1SMcG0013084 Contig15794uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30023357h1SMcG0013084 Contig15794newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30023357 vs. Planmine SMEST
Match: SMESG000046304.1 (SMESG000046304.1)

HSP 1 Score: 285.419 bits (729), Expect = 2.925e-92
Identity = 143/179 (79.89%), Postives = 149/179 (83.24%), Query Frame = 2 
Query:    2 DWLMID*KNLISICQGYKSSSPTYKDHKSNMTKKINAISVQPVQMFHNYKMYFLKEPINMQLVNPVKLNKTQFQSLAGTLSMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTITIQGYKADQNDVLSPIWKIVTARLSQLF*CIVFNKCINVSLLFYKQ 538
            DWL       ISICQGYKSSSP YKDHKSNMTKKI+AISVQPVQMFHNYKMY LKEPINMQL NPVKLNKTQFQSLAGTLSM+DIKDID  FKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTI IQGYKADQNDVLSPIWKI          C++    +  SLLFY +
Sbjct:    5 DWL-------ISICQGYKSSSPLYKDHKSNMTKKISAISVQPVQMFHNYKMYILKEPINMQLANPVKLNKTQFQSLAGTLSMIDIKDIDTVFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTIAIQGYKADQNDVLSPIWKI----------CLI--NVLMFSLLFYNE 164
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BLAST of SMED30023357 vs. Planmine SMEST
Match: SMESG000066383.1 (SMESG000066383.1)

HSP 1 Score: 278.485 bits (711), Expect = 4.922e-87
Identity = 133/143 (93.01%), Postives = 136/143 (95.10%), Query Frame = 2 
Query:   50 YKSSSPTYKDHKSNMTKKINAISVQPVQMFHNYKMYFLKEPINMQLVNPVKLNKTQFQSLAGTLSMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTITIQGYKADQNDVLSPIWKIVTARLSQ 478
            YKS+SP YKDHKSNMTKKI   SVQPVQMFHNYKMYFLKEPINMQ  NPVKLNKT+FQSLAGTLSMLDIKDI NTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWY+TITIQGYKADQNDVLSPIWKIVTARLSQ
Sbjct:  714 YKSASPPYKDHKSNMTKKI---SVQPVQMFHNYKMYFLKEPINMQFANPVKLNKTKFQSLAGTLSMLDIKDIGNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYITITIQGYKADQNDVLSPIWKIVTARLSQ 853
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BLAST of SMED30023357 vs. Planmine SMEST
Match: SMESG000060524.1 (SMESG000060524.1)

HSP 1 Score: 213.386 bits (542), Expect = 3.792e-70
Identity = 102/128 (79.69%), Postives = 113/128 (88.28%), Query Frame = 2 
Query:    2 DWLMID*KNLISICQGYKSSSPTYKDHKSNMTKKINAISVQPVQMFHNYKMYFLKEPINMQLVNPVKLNKTQFQSLAGTLSMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQEN 385
            DWL       I+ICQGYK+S P YKD+KSNMTKKINAI+VQPVQM HNY+MYFL+EPIN QL NPVKL++TQFQ+LA TLSM+DIKDID  FKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKE+EN
Sbjct:   30 DWL-------INICQGYKTSLPLYKDNKSNMTKKINAINVQPVQMLHNYQMYFLREPINTQLSNPVKLHRTQFQTLAATLSMIDIKDIDTVFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEREN 150
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BLAST of SMED30023357 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 203.371 bits (516), Expect = 1.377e-59
Identity = 96/103 (93.20%), Postives = 98/103 (95.15%), Query Frame = 2 
Query:  176 NMQLVNPVKLNKTQFQSLAGTLSMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTITIQGYKADQNDVLSPIWKIVTARLSQLF 484
            NMQL NPVKLNKTQFQSLAGTLSM+DIKDID  FK INSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWY+TITIQGYKADQNDVLSPIWKIVTAR SQLF
Sbjct:  841 NMQLANPVKLNKTQFQSLAGTLSMIDIKDIDTVFKNINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYVTITIQGYKADQNDVLSPIWKIVTARFSQLF 943
[Close]
BLAST of SMED30023357 vs. Planmine SMEST
Match: SMESG000058180.1 (SMESG000058180.1)

HSP 1 Score: 203.371 bits (516), Expect = 1.480e-59
Identity = 96/103 (93.20%), Postives = 98/103 (95.15%), Query Frame = 2 
Query:  176 NMQLVNPVKLNKTQFQSLAGTLSMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYLTITIQGYKADQNDVLSPIWKIVTARLSQLF 484
            NMQL NPVKLNKTQFQSLAGTLSM+DIKDID  FK INSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWY+TITIQGYKADQNDVLSPIWKIVTAR SQLF
Sbjct:  832 NMQLANPVKLNKTQFQSLAGTLSMIDIKDIDTVFKNINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWYVTITIQGYKADQNDVLSPIWKIVTARFSQLF 934
The following BLAST results are available for this feature:
BLAST of SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 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 SMED30023357 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046304.12.925e-9279.89SMESG000046304.1[more]
SMESG000066383.14.922e-8793.01SMESG000066383.1[more]
SMESG000060524.13.792e-7079.69SMESG000060524.1[more]
SMESG000058180.11.377e-5993.20SMESG000058180.1[more]
SMESG000058180.11.480e-5993.20SMESG000058180.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023357 ID=SMED30023357|Name=SMED30023357|organism=Schmidtea mediterranea sexual|type=transcript|length=799bp
TGATTGGCTAATGATTGATTAAAAAAACTTAATCAGTATCTGTCAAGGGT
ATAAAAGCTCGTCACCAACTTATAAAGATCATAAATCAAACATGACCAAG
AAAATCAATGCTATCAGTGTCCAACCAGTTCAGATGTTCCACAATTATAA
AATGTATTTTTTAAAGGAGCCTATCAATATGCAATTGGTAAATCCAGTCA
AACTCAATAAAACTCAATTTCAATCTCTTGCTGGGACTCTCTCAATGTTA
GATATCAAGGATATTGATAATACGTTCAAAAAGATCAATTCCAATTTAAA
ATGCAATGAAAATGCTTTCTTCACGAGTCAATATACCAGATATTATGATG
CATTTACAGAAATAGGTTTCAAAGAACAGGAAAACTGGTATTTAACAATA
ACAATCCAAGGATATAAAGCTGATCAAAATGATGTGCTTTCTCCAATCTG
GAAAATTGTTACTGCTAGACTTTCACAGTTATTTTAATGTATAGTGTTTA
ATAAATGTATTAATGTTTCTTTGTTATTCTATAAACAAAATTATAAGTAG
TTTTAAAATAGTGTTAAAATGATGTCTGAAAAAGGTAAAATATAAAATAT
AAATAATTAATTAATTTTGGTTTAGAATATTTAATAAACTTTTTGTTTGA
TAAACTTGAAGAAATAACCGGTGTAAAAATTAGAGATATGTTGACTCTAG
TTGAAGCATTGAGTAAAGAATCGGATTGCGAATCTGAATGTCAGAGTGAT
GAAATTGTTAATGATACTGAAATTATTAATGATTCTGAAGAAATTATTA
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protein sequence of SMED30023357-orf-1

>SMED30023357-orf-1 ID=SMED30023357-orf-1|Name=SMED30023357-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
MTKKINAISVQPVQMFHNYKMYFLKEPINMQLVNPVKLNKTQFQSLAGTL
SMLDIKDIDNTFKKINSNLKCNENAFFTSQYTRYYDAFTEIGFKEQENWY
LTITIQGYKADQNDVLSPIWKIVTARLSQLF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR013809ENTH