SMED30004705

Overview
NameSMED30004705
Smed IDSMED30004705
Length (bp)325
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 SMED30004705 (SMED30004705) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004705 (SMED30004705) 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 SMED30004705 (SMED30004705) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004705 (SMED30004705) 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




SMED30004705

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



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30004705h1SMcG0006318 Contig4800uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004705h1SMcG0006318 Contig4800newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004705h1SMcG0007112 Contig4800uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004705h1SMcG0007112 Contig4800newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30004705h1SMcG0006318 Contig45430uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004705h1SMcG0006318 Contig45430newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004705h1SMcG0006318 Contig4800uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004705h1SMcG0006318 Contig4800newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30004705h1SMcG0006318 dd_Smed_v4_4752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30004705h1SMcG0006318 dd_Smed_v4_4752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30004705h1SMcG0006318 dd_Smed_v4_4752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30004705h1SMcG0006318 dd_Smed_v4_4752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30004705h1SMcG0006318 dd_Smed_v4_4752_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004705h1SMcG0007112 Contig4800uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004705h1SMcG0007112 Contig4800newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 2 cellSMED30004705h1SMcG0006318 dd_Smed_v4_4752_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
SMED30004705 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.053649:701..1025 -1625
v31.013204:13185..13679 +1526
Homology
BLAST of SMED30004705 vs. TrEMBL
Match: A0A183PFR8 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS13203 PE=4 SV=1)

HSP 1 Score: 77.411 bits (189), Expect = 3.809e-14
Identity = 42/98 (42.86%), Postives = 60/98 (61.22%), Query Frame = -1
Query:    2 EPEADELTPLPRNYKIES-SHNPHRKLEGSLPDVSY--------------CNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 250
            +PE+ +L PLP++Y IES  H P    E S+PD+S               C   +     +++R+E ++LSQ RRQE+ HE ER++RGEIVIR+ADIK
Sbjct:  842 DPESPDLLPLPKSYVIESIVHLPGAVKEASMPDISINRGHTAGRYDSPSRCTAAQQPVSGVLTREEVARLSQARRQELYHEMERRKRGEIVIRLADIK 939          
BLAST of SMED30004705 vs. TrEMBL
Match: A0A183K9R3 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS11746 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 3.971e-14
Identity = 42/98 (42.86%), Postives = 60/98 (61.22%), Query Frame = -1
Query:    2 EPEADELTPLPRNYKIES-SHNPHRKLEGSLPDVSY--------------CNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 250
            +PE+ +L PLP++Y IES  H P    E S+PD+S               C   +     +++R+E ++LSQ RRQE+ HE ER++RGEIVIR+ADIK
Sbjct:  511 DPESPDLLPLPKSYVIESIVHLPGAVKEASMPDISINRGHTAGRYDSPSRCTAAQQPVSGVLTREEVARLSQARRQELYHEMERRKRGEIVIRLADIK 608          
BLAST of SMED30004705 vs. TrEMBL
Match: A0A183LA56 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS681 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 4.804e-14
Identity = 42/98 (42.86%), Postives = 60/98 (61.22%), Query Frame = -1
Query:    2 EPEADELTPLPRNYKIES-SHNPHRKLEGSLPDVSY--------------CNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 250
            +PE+ +L PLP++Y IES  H P    E S+PD+S               C   +     +++R+E ++LSQ RRQE+ HE ER++RGEIVIR+ADIK
Sbjct:  817 DPESPDLLPLPKSYVIESIVHLPGAVKEASMPDISINRGHTAGRYDSPSRCTAAQQPVSGVLTREEVARLSQARRQELYHEMERRKRGEIVIRLADIK 914          
BLAST of SMED30004705 vs. TrEMBL
Match: A0A095BXM5 (Junctophilin-1 OS=Schistosoma haematobium OX=6185 GN=MS3_01977 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 5.029e-14
Identity = 42/98 (42.86%), Postives = 60/98 (61.22%), Query Frame = -1
Query:    2 EPEADELTPLPRNYKIES-SHNPHRKLEGSLPDVSY--------------CNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 250
            +PE+ +L PLP++Y IES  H P    E S+PD+S               C   +     +++R+E ++LSQ RRQE+ HE ER++RGEIVIR+ADIK
Sbjct:  958 DPESPDLLPLPKSYVIESIVHLPGAVKEASMPDISINRGHTAGRYDSPSRCTAAQQPVSGVLTREEVARLSQARRQELYHEMERRKRGEIVIRLADIK 1055          
BLAST of SMED30004705 vs. TrEMBL
Match: A0A430QMN6 (Junctophilin OS=Schistosoma bovis OX=6184 GN=DC041_0007199 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 6.055e-14
Identity = 42/98 (42.86%), Postives = 60/98 (61.22%), Query Frame = -1
Query:    2 EPEADELTPLPRNYKIES-SHNPHRKLEGSLPDVSY--------------CNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 250
            +PE+ +L PLP++Y IES  H P    E S+PD+S               C   +     +++R+E ++LSQ RRQE+ HE ER++RGEIVIR+ADIK
Sbjct:  864 DPESPDLLPLPKSYVIESIVHLPGAVKEASMPDISINRGHTAGRYDSPSRCTAAQQPVSGVLTREEVARLSQARRQELYHEMERRKRGEIVIRLADIK 961          
BLAST of SMED30004705 vs. Planmine SMEST
Match: SMESG000001306.1 (SMESG000001306.1)

HSP 1 Score: 200.675 bits (509), Expect = 2.129e-61
Identity = 97/98 (98.98%), Postives = 98/98 (100.00%), Query Frame = -1
Query:    2 SSRLIGKRIQNPLNIEPEADELTPLPRNYKIESSHNPHRKLEGSLPDVSYCNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 295
            S+RLIGKRIQNPLNIEPEADELTPLPRNYKIESSHNPHRKLEGSLPDVSYCNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK
Sbjct:  752 SNRLIGKRIQNPLNIEPEADELTPLPRNYKIESSHNPHRKLEGSLPDVSYCNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEIVIRMADIK 849          
The following BLAST results are available for this feature:
BLAST of SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183PFR83.809e-1442.86Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A183K9R33.971e-1442.86Uncharacterized protein OS=Schistosoma curassoni O... [more]
A0A183LA564.804e-1442.86Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A095BXM55.029e-1442.86Junctophilin-1 OS=Schistosoma haematobium OX=6185 ... [more]
A0A430QMN66.055e-1442.86Junctophilin OS=Schistosoma bovis OX=6184 GN=DC041... [more]
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BLAST of SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 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 SMED30004705 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000001306.12.129e-6198.98SMESG000001306.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004705 ID=SMED30004705|Name=SMED30004705|organism=Schmidtea mediterranea sexual|type=transcript|length=325bp
CTTTTATATCTGCCATTCTGATAACGATTTCACCGCGTCGCTGTCGTTCT
TGTTCATGAAGAATTTCTTGGCGTCTTTGTTGACTCAATTGTGAAGCTTC
TTGGCGGGACATTAAGGTTCCAGTTTTGGTTTTGATTTCATTACAATAGG
ACACATCAGGAAGACTTCCTTCTAACTTCCGGTGAGGATTGTGTGATGAT
TCAATTTTATAATTTCGAGGTAAGGGTGTCAATTCATCTGCCTCGGGTTC
AATGTTCAATGGATTTTGTATTCTTTTGCCGATTAGTCGACTGGAAAAAT
TATTTTGAAATAAAGGAAAAATCAG
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protein sequence of SMED30004705-orf-1

>SMED30004705-orf-1 ID=SMED30004705-orf-1|Name=SMED30004705-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp
LIFPLFQNNFSSRLIGKRIQNPLNIEPEADELTPLPRNYKIESSHNPHRK
LEGSLPDVSYCNEIKTKTGTLMSRQEASQLSQQRRQEILHEQERQRRGEI
VIRMADIK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell