SMED30026002

Overview
NameSMED30026002
Smed IDSMED30026002
Length (bp)599
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 SMED30026002 (SMED30026002) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026002 (SMED30026002) 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



SMED30026002

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



PAGE Curations: 41

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30026002h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30026002h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30026002h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30026002h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
secretory cellSMED30026002h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30026002h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30026002h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30026002h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30026002h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30026002h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30026002h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30026002h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30026002h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30026002h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30026002h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30026002h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30026002h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30026002h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30026002h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
secretory cellSMED30026002h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30026002h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30026002h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30026002h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30026002h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30026002h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
pigment cellSMED30026002h1SMcG0014660 SmedASXL_008102SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30026002h1SMcG0014660 dd_Smed_v4_1555_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30026002h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30026002h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30026002h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30026002h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30026002h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026002h1SMcG0014660 Contig11338uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30026002h1SMcG0014660 Contig11338newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30026002h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30026002h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
GABAergic neuronSMED30026002h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30026002h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30026002h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30026002h1SMcG0014660 dd_Smed_v4_1555_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30026002h1SMcG0014660 dd_Smed_v4_587_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
SMED30026002 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001151:49448..50042 -2845
Homology
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BLAST of SMED30026002 vs. TrEMBL
Match: A0A0L8IHE5 (DDE_Tnp_IS1595 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22024389mg PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 2.543e-10
Identity = 49/175 (28.00%), Postives = 83/175 (47.43%), Query Frame = 2 
Query:   77 ISTGQPFATCQYGFAYVVTDSPDGHVFRCERYKKRKNICVGSFFEKVKLPIRSIL*ILFHWLTYVPVMTAAELSNAGTSI-----------YLTNVADRSANTLLPFIQQ*VIPGSVIESDE*AATINCRPXXXXXXXXXXXXXXXX-XXGACINHVESFWSQMSNKACLPTPSA 565
            I+T + F    +        S +G V+RC   +K  +I   +F EK KL ++ I  I+FH++   P+ TAA  +                 +L  V DRSA TL   + + V+PG+++ +D+ A+  N +    I      S       +GAC NH+E++WS++  +    T S+
Sbjct:   27 IATCKTFVCTHFMTLKKSARSLNGFVWRCGNCRKNISIRTKTFMEKSKLSLQKIFHIVFHFVFEAPIFTAALYTGVDNKTAIQWYEFLSRRFLQRVPDRSAATLEGVMIENVLPGTLVHTDKWASYRNLQQLSYIHRTVNHSTNFVDPKTGACTNHIEAYWSRIKRRLKYVTGSS 201
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BLAST of SMED30026002 vs. TrEMBL
Match: A0A183A3J7 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS1532 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.744e-8
Identity = 37/100 (37.00%), Postives = 57/100 (57.00%), Query Frame = 2 
Query:  137 SPDGHVFRCERYKKRKNICVGSFFEKVKLPIRSIL*ILFHWLTYVPVMTAAELSNAG--TSI-YLTNVADRSANTLLPFIQQ*VIPGSVIESDE*AATIN 427
            SPDG VFRC   KKR +I  G+FFEK +LP+ +++ ++F+++   PV  AA ++N    +SI + T   D  ++ +     Q    GS +E DE  A  N
Sbjct:    9 SPDGFVFRCTHCKKRMSIRSGTFFEKSRLPLTTLMELMFYFVMEEPVTRAAAMANVSRKSSIQWYTYCRDVCSSVMCSLPTQLGGVGSTVEVDESVAVKN 108
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BLAST of SMED30026002 vs. TrEMBL
Match: A0A0L8HC94 (DDE_Tnp_IS1595 domain-containing protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22017762mg PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 4.072e-7
Identity = 46/160 (28.75%), Postives = 73/160 (45.62%), Query Frame = 2 
Query:  137 SPDGHVFRCERYKKRKNICVGSFFEKVKLPIRSIL*ILFHWLTYVPVMTAA---------------------------ELSNAGTSIYLTNVADRSANTLLPFIQQ*VIPGSVIESDE*AATINCRPXXXXXXXXXXXXXXXX-XXGACINHVESFWSQM 532
            S DG V+RC   KK  +I   +F EK KL ++ I  I+FH++   P+ T A                           + +  G   +L  V DRSA TL   I + V+PG+++ +D+ A+  N +    I      S       +GAC N +E++WS++
Sbjct:   47 SLDGFVWRCGNCKKNISIRTKTFMEKSKLSLQKIFHIVFHFVFEAPISTTALYTGVDNKTVIQWYEFCREVCSGKMLRDKAPLGGPGFLQRVPDRSAATLEAVIIENVLPGTIVHTDKWASYRNLQQLGYIHRAVNQSTNFVDPETGACTNRIEAYWSRI 206
[Close]
BLAST of SMED30026002 vs. TrEMBL
Match: A0A2P4VMW6 (DDE_Tnp_IS1595 domain-containing protein OS=Caenorhabditis remanei OX=31234 GN=FL81_24642 PE=4 SV=1)

HSP 1 Score: 48.1358 bits (113), Expect = 9.482e-6
Identity = 39/104 (37.50%), Postives = 53/104 (50.96%), Query Frame = 2 
Query:  143 DGHVFRC---ERYKKRKNICV--GSFFEKVKLPIRSIL*ILFHWLTYVPVMTAAELSNA-GTS------IYLTNVADRSANTLLPFIQQ*VIPGSVIESDE*AA 418
            D HV+RC    R K+   I +  GSFFE +KL +  +  +   W+   P  T  E+S   G S      + +  V +RSA TLLP + + V PGS I SD  AA
Sbjct:  114 DKHVWRCLPCRRNKESSKISMRAGSFFENLKLTVVEVFYLAAEWIEN-PSKTVXEVSKQFGISHTTVVEVVMFRVPNRSAATLLPIVAKYVEPGSKIISDGWAA 216

HSP 2 Score: 29.261 bits (64), Expect = 9.482e-6
Identity = 12/25 (48.00%), Postives = 17/25 (68.00%), Query Frame = 1 
Query:  412 GSYNQLQALDFNHITVNYQRNFVDP 486
             +Y  L A+ F+H  VN++ NFVDP
Sbjct:  215 AAYTGLSAMQFDHHWVNHKINFVDP 239
The following BLAST results are available for this feature:
BLAST of SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A0L8IHE52.543e-1028.00DDE_Tnp_IS1595 domain-containing protein OS=Octopu... [more]
A0A183A3J71.744e-837.00Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A0L8HC944.072e-728.75DDE_Tnp_IS1595 domain-containing protein OS=Octopu... [more]
A0A2P4VMW69.482e-637.50DDE_Tnp_IS1595 domain-containing protein OS=Caenor... [more]
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BLAST of SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 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 SMED30026002 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026002 ID=SMED30026002|Name=SMED30026002|organism=Schmidtea mediterranea sexual|type=transcript|length=599bp
TTTTTTATTGTTCATTGTTTAAGTTAACTCTGTTTTAGTGCGTGATGGAC
TCGCCTAGCGTTCAACTGTTTCGTCGATTTCAACAGGACAACCATTCGCT
ACCTGTCAATATGGTTTTGCATATGTGGTCACTGACAGCCCGGATGGTCA
TGTGTTTCGCTGTGAAAGATACAAGAAGCGTAAAAACATTTGCGTGGGAA
GTTTCTTTGAAAAAGTGAAGTTGCCAATTCGGTCCATTTTGTAAATTCTC
TTTCATTGGCTAACATATGTCCCAGTCATGACAGCGGCAGAATTGTCAAA
TGCGGGAACAAGCATCTATCTCACAAACGTGGCGGATAGATCTGCCAATA
CCCTCCTGCCGTTCATCCAACAATGAGTTATTCCTGGGTCTGTCATTGAG
TCCGACGAGTAGGCAGCTACAATCAACTGCAGGCCCTGGATTTCAATCAC
ATAACTGTCAACTATCAGCGCAATTTTGTGGACCCTCAGTGGTGCGTGTA
TAAATCATGTCGAGTCGTTCTGGTCTCAAATGTCAAATAAAGCGTGTCTG
CCGACTCCCAGCGCGATTTGGGAACGGTTCCTTACGCTTACACCTGATT
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