LPT

Overview
NameLPT
Smed IDSMED30005889
Length (bp)639
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 LPT (SMED30005889) t-SNE clustered cells

Violin plots show distribution of expression levels for LPT (SMED30005889) 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



SMED30005889

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



PAGE Curations: 22

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30005889SMESG000040592.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30005889SMESG000040592.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30005889SMESG000040592.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005889SMESG000040592.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30005889SMESG000040592.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
central nervous systemSMED30005889SMESG000040592.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30005889SMESG000035457.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30005889SMESG000035457.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30005889SMESG000035457.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30005889SMESG000035457.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30005889SMESG000035457.1 Contig5422newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
central nervous systemSMED30005889SMESG000035457.1 Contig5422uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
Smed sexual biotypeSMED30005889SMESG000040592.1 Contig47362newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30005889SMESG000040592.1 Contig47362uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30005889SMESG000040592.1 KX681482smed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30005889SMESG000040592.1 KX681482smed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30005889SMESG000040592.1 KX681482smed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30005889SMESG000040592.1 KX681482smed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30005889SMESG000040592.1 LPTsmed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
neoblastSMED30005889SMESG000040592.1 LPTsmed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymaSMED30005889SMESG000040592.1 LPTsmed_ncbi_20200123PMID:30194301
Mihaylova et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
epidermisSMED30005889SMESG000040592.1 dd_Smed_v4_5095_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
Homology
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BLAST of LPT vs. TrEMBL
Match: A0A1S5XVZ9 (LPT OS=Schmidtea mediterranea OX=79327 GN=LPT PE=2 SV=1)

HSP 1 Score: 323.939 bits (829), Expect = 1.421e-98
Identity = 195/211 (92.42%), Postives = 198/211 (93.84%), Query Frame = 1 
Query:    7 LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGXXXXXXXXXXXXXDMVQNRNPYRQNTLNPQSAXXXXXXXXXXXXQLDIXXXXXXXXXXXXXXXHSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA 639
            LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGQQKYQQQ Q    DMVQNRNPYRQNTLNPQSANSG  +S+S+  QLDISGMSGMSGMPG    HSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA
Sbjct: 2626 LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGQQKYQQQQQ----DMVQNRNPYRQNTLNPQSANSGSGNSSSN--QLDISGMSGMSGMPGS---HSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA 2827
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BLAST of LPT vs. Planmine SMEST
Match: SMESG000040592.1 (SMESG000040592.1)

HSP 1 Score: 323.939 bits (829), Expect = 3.657e-102
Identity = 195/211 (92.42%), Postives = 198/211 (93.84%), Query Frame = 1 
Query:    7 LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGXXXXXXXXXXXXXDMVQNRNPYRQNTLNPQSAXXXXXXXXXXXXQLDIXXXXXXXXXXXXXXXHSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA 639
            LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGQQKYQQQ Q    DMVQNRNPYRQNTLNPQSANSG  +S+S+  QLDISGMSGMSGMPG    HSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA
Sbjct: 2608 LMDQGCRSASHMMPINIVPGNSYLGQSKFVPGQQKYQQQQQ----DMVQNRNPYRQNTLNPQSANSGSGNSSSN--QLDISGMSGMSGMPGS---HSNSIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPHKFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQNPSGPGTPQSPCAA 2809
The following BLAST results are available for this feature:
BLAST of LPT 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 LPT 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 LPT 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 LPT 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 LPT 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 LPT 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 LPT 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 LPT vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A1S5XVZ91.421e-9892.42LPT OS=Schmidtea mediterranea OX=79327 GN=LPT PE=2... [more]
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BLAST of LPT 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 LPT 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 LPT 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 LPT 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 LPT 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 LPT vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000040592.13.657e-10292.42SMESG000040592.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005889 ID=SMED30005889|Name=LPT|organism=Schmidtea mediterranea sexual|type=transcript|length=639bp
GCGGCATTAATGGATCAGGGCTGCAGATCGGCATCTCACATGATGCCGAT
CAATATTGTGCCTGGCAACAGCTATCTGGGCCAGAGCAAATTTGTCCCCG
GCCAACAGAAATATCAGCAGCAGCACCAACAGCACCAACAAGATATGGTG
CAAAATCGCAATCCTTACAGACAGAATACATTGAATCCACAATCAGCCAA
TAGCGGCGGCAGCAGTAGCAATAGTAGCAATAACCAATTGGATATCTCTG
GCATGTCTGGCATGTCTGGCATGCCCGGCATGCCCGGCTCCCACTCGAAT
TCCATCGGGGAGGAGTGTGTGCAAATGTCTGCCGATCCAAATGCCAGCAA
CATTATCCACATGGACACGAGAATGTCACCGAATATCATCCAGCACCAGT
CGCCCATTTCCCCGTTCACTCACATGTCACAATCGCAACTACCACCACAC
AAGTTCCAGCAGCCCTCTAGGCCGATATCGACTGGCCTCAACAAATCATT
TGACCTATCAGGAGGTTGCCAAATGTACATTGCAGCCCATTCACCACGCG
ACAGCCACACTCCCCAGAGCTCTGCTCCATCCAACCAGCCAATGCAGAAC
CCATCTGGCCCTGGCACCCCTCAGAGCCCCTGTGCCGCC
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protein sequence of SMED30005889-orf-1

>SMED30005889-orf-1 ID=SMED30005889-orf-1|Name=SMED30005889-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=213bp
AALMDQGCRSASHMMPINIVPGNSYLGQSKFVPGQQKYQQQHQQHQQDMV
QNRNPYRQNTLNPQSANSGGSSSNSSNNQLDISGMSGMSGMPGMPGSHSN
SIGEECVQMSADPNASNIIHMDTRMSPNIIQHQSPISPFTHMSQSQLPPH
KFQQPSRPISTGLNKSFDLSGGCQMYIAAHSPRDSHTPQSSAPSNQPMQN
PSGPGTPQSPCAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000103central nervous system
PLANA:0000429neoblast
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 174..204
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 165..204