SMED30022739

Overview
NameSMED30022739
Smed IDSMED30022739
Length (bp)469
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 SMED30022739 (SMED30022739) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022739 (SMED30022739) 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 SMED30022739 (SMED30022739) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022739 (SMED30022739) 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



SMED30022739

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30022739h1SMcG0006567 Contig6905uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30022739h1SMcG0006567 Contig6905newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30022739h1SMcG0006563 Contig907newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30022739h1SMcG0009497 Contig907newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30022739h1SMcG0006563 Contig3349GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30022739h1SMcG0006563 dd_Smed_v4_11479_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30022739h1SMcG0006568 dd_Smed_v4_5607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022739h1SMcG0006568 dd_Smed_v4_5607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022739h1SMcG0006568 dd_Smed_v4_5607_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022739h1SMcG0006563 Contig55219uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30022739h1SMcG0006563 Contig55219newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30022739h1SMcG0006568 dd_Smed_v6_5607_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30022739h1SMcG0006568 Contig52462newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30022739h1SMcG0006568 Contig52462uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30022739h1SMcG0006568 Contig52462newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30022739h1SMcG0006568 Contig52462uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30022739h1SMcG0006568 Contig52462newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30022739h1SMcG0006568 Contig52462uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30022739h1SMcG0006568 dd_Smed_v4_5607_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022739 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012601:13650..14167 -2319
v31.005711:42059..42577 -2280
v31.037954:983..1498 -1896
v31.016018:8543..9058 -1866
v31.016607:12891..13406 +1830
v31.016607:11661..12176 +1785
Homology
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BLAST of SMED30022739 vs. Planmine SMEST
Match: SMESG000033476.1 (SMESG000033476.1)

HSP 1 Score: 314.694 bits (805), Expect = 7.106e-112
Identity = 154/156 (98.72%), Postives = 156/156 (100.00%), Query Frame = 1 
Query:    1 MGIRGLYSYFAFDMKAYTIFNLVQKAKVVKNMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLTALENLK 468
            MGIRGLYSYFAFDMKAYTIFNLVQKAKVVK+MEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECC+NKMPFKDLGNVRSMFNVLTALENLK
Sbjct:    1 MGIRGLYSYFAFDMKAYTIFNLVQKAKVVKDMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCQNKMPFKDLGNVRSMFNVLTALENLK 156
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BLAST of SMED30022739 vs. Planmine SMEST
Match: SMESG000033476.1 (SMESG000033476.1)

HSP 1 Score: 319.316 bits (817), Expect = 5.127e-108
Identity = 154/156 (98.72%), Postives = 156/156 (100.00%), Query Frame = 1 
Query:    1 MGIRGLYSYFAFDMKAYTIFNLVQKAKVVKNMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLTALENLK 468
            MGIRGLYSYFAFDMKAYTIFNLVQKAKVVK+MEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECC+NKMPFKDLGNVRSMFNVLTALENLK
Sbjct:    1 MGIRGLYSYFAFDMKAYTIFNLVQKAKVVKDMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCQNKMPFKDLGNVRSMFNVLTALENLK 156
[Close]
BLAST of SMED30022739 vs. Planmine SMEST
Match: SMESG000033476.1 (SMESG000033476.1)

HSP 1 Score: 287.345 bits (734), Expect = 3.294e-101
Identity = 141/143 (98.60%), Postives = 143/143 (100.00%), Query Frame = 1 
Query:   40 MKAYTIFNLVQKAKVVKNMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLTALENLK 468
            MKAYTIFNLVQKAKVVK+MEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECC+NKMPFKDLGNVRSMFNVLTALENLK
Sbjct:    1 MKAYTIFNLVQKAKVVKDMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCQNKMPFKDLGNVRSMFNVLTALENLK 143
[Close]
BLAST of SMED30022739 vs. Planmine SMEST
Match: SMESG000033476.1 (SMESG000033476.1)

HSP 1 Score: 291.582 bits (745), Expect = 2.079e-97
Identity = 141/143 (98.60%), Postives = 143/143 (100.00%), Query Frame = 1 
Query:   40 MKAYTIFNLVQKAKVVKNMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLTALENLK 468
            MKAYTIFNLVQKAKVVK+MEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECC+NKMPFKDLGNVRSMFNVLTALENLK
Sbjct:    1 MKAYTIFNLVQKAKVVKDMEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCQNKMPFKDLGNVRSMFNVLTALENLK 143
[Close]
BLAST of SMED30022739 vs. Planmine SMEST
Match: SMESG000033479.1 (SMESG000033479.1)

HSP 1 Score: 186.808 bits (473), Expect = 3.982e-57
Identity = 93/125 (74.40%), Postives = 102/125 (81.60%), Query Frame = 1 
Query:   94 MEILVDFRSFRRDLDKLILRKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSLDEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLTALENLK 468
            MEILVDF SFRR LD++ILRKII DFDN++LSISCVECDIF KAYLEFH+MFAEIGIKLVWIYDGI  LDEV+  +KSETW  RI  YSN VD  LECCKNKMP K+  +V S    LTALENLK
Sbjct:    1 MEILVDFSSFRRGLDEIILRKIINDFDNDFLSISCVECDIFSKAYLEFHRMFAEIGIKLVWIYDGIKGLDEVVHNEKSETWSYRINKYSNSVDAVLECCKNKMPVKNFKDVISWAYSLTALENLK 125
The following BLAST results are available for this feature:
BLAST of SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 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 SMED30022739 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033476.17.106e-11298.72SMESG000033476.1[more]
SMESG000033476.15.127e-10898.72SMESG000033476.1[more]
SMESG000033476.13.294e-10198.60SMESG000033476.1[more]
SMESG000033476.12.079e-9798.60SMESG000033476.1[more]
SMESG000033479.13.982e-5774.40SMESG000033479.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022739 ID=SMED30022739|Name=SMED30022739|organism=Schmidtea mediterranea sexual|type=transcript|length=469bp
ATGGGTATAAGGGGACTTTATTCGTATTTTGCTTTTGACATGAAAGCTTA
TACCATTTTTAATTTAGTTCAAAAAGCTAAAGTTGTCAAAAACATGGAAA
TTTTAGTAGATTTCAGATCATTTCGTAGAGATCTTGATAAACTTATTTTG
CGAAAAATAATTAAAGACTTTGACAATAATTATTTATCCATATCCTGTGT
TGAATGTGATATTTTTGGTAAAGCATATTTGGAATTCCACAAAATGTTTG
CCGAAATTGGAATTAAATTGGTGTGGATTTATGATGGGATAAATAGCTTA
GACGAAGTTATGTGTTATCAAAAATCAGAAACATGGGATTGTCGAATTAA
AAATTATTCTAATTTGGTTGATAAATTTCTTGAATGTTGCAAAAATAAAA
TGCCTTTTAAAGATTTGGGAAATGTTCGTTCGATGTTCAATGTTTTGACT
GCTCTCGAGAATTTGAAAG
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protein sequence of SMED30022739-orf-1

>SMED30022739-orf-1 ID=SMED30022739-orf-1|Name=SMED30022739-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
MGIRGLYSYFAFDMKAYTIFNLVQKAKVVKNMEILVDFRSFRRDLDKLIL
RKIIKDFDNNYLSISCVECDIFGKAYLEFHKMFAEIGIKLVWIYDGINSL
DEVMCYQKSETWDCRIKNYSNLVDKFLECCKNKMPFKDLGNVRSMFNVLT
ALENLK
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