SMED30027566

Overview
NameSMED30027566
Smed IDSMED30027566
Length (bp)1664
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 SMED30027566 (SMED30027566) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027566 (SMED30027566) 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 SMED30027566 (SMED30027566) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027566 (SMED30027566) 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



SMED30027566

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



PAGE Curations: 18

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30027566h1SMcG0014763 SmedASXL_011946SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30027566h1SMcG0014763 SmedASXL_011946SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027566h1SMcG0014763 Contig39242newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30027566h1SMcG0014763 Contig39242uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parapharyngeal regionSMED30027566h1SMcG0014763 dd_Smed_v6_7519_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30027566h1SMcG0014763 dd_Smed_v4_7519_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027566h1SMcG0014763 SMED_01064_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30027566h1SMcG0014763 SMED_01064_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027566 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006413:4777..6559 -8053
Homology
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BLAST of SMED30027566 vs. Planmine SMEST
Match: SMESG000075236.1 (SMESG000075236.1)

HSP 1 Score: 381.333 bits (978), Expect = 8.635e-128
Identity = 184/185 (99.46%), Postives = 185/185 (100.00%), Query Frame = 3 
Query:  990 AYSDDFKRQMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE 1544
            AYSDDFK+QMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE
Sbjct:  251 AYSDDFKQQMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE 435
[Close]
BLAST of SMED30027566 vs. Planmine SMEST
Match: SMESG000075236.1 (SMESG000075236.1)

HSP 1 Score: 381.333 bits (978), Expect = 1.027e-127
Identity = 184/185 (99.46%), Postives = 185/185 (100.00%), Query Frame = 3 
Query:  990 AYSDDFKRQMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE 1544
            AYSDDFK+QMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE
Sbjct:  250 AYSDDFKQQMEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVIESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTEFNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGDTERIFRYSVSDLPLEAVLKDDSIVLE 434
The following BLAST results are available for this feature:
BLAST of SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 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 SMED30027566 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000075236.18.635e-12899.46SMESG000075236.1[more]
SMESG000075236.11.027e-12799.46SMESG000075236.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027566 ID=SMED30027566|Name=SMED30027566|organism=Schmidtea mediterranea sexual|type=transcript|length=1664bp
GATTTTTATAAGTAAATATCTTCAATTTTAATAAAAATCTGATATTTAAA
AGTTACATAATCACCCATAGAGAAATTTATTTATATTGCTTTGTTTCGTA
ATCAATGTCAATTATTACATAATAACTTTTTAACCTAGTCAATGTCACTT
GGCTGTCTAGTAATGTTTAAATAATCATTTTTATTTAGTAAAATGGCATA
AAATATAGAATTATTAAATGGGGTATGAAATTTGTACCTTTTGTCACCCA
AGCCTAGATTGGAATATAAATTATCGATTGGTCATGCGATCAAGAACAAT
TGTGCTCTGTTTATGTGAAATTTGAATGATTATATTTTCAGTGCATATAT
GGATATTGCTCCATGTTTTCTCACGTAACAAGTCATGAATTTATCTTTGG
CCTCCCGTTAAAATTTATGCAAACATTAAGAAAGGGCCAGTGATGGCCCT
CGCCGAATTTGTTTTTAAATTTTTATGATTTTTTAATTATTATCGATATT
TCCAATGATAATAACGGATATTTGGTGGTAATTTCTCAAATGCAATTGTT
AGCGATCAGCTGGTGATGATTTATTATTATTTTGTTATAATCACTTTTTA
TTGGTTAAATTAAACGACCAATAGAATTTCAATTTAATGAAAATTTGAAA
TCTGTAACAATGATTTTTCTATCTACTCATTTTAGTCTTTTTATTTATTC
ACGGGAATTTTCTACAATTGTGGCAAATTTAAGGGGGGTTCCTGTCCTCT
TTGTTTTAATTTTTATATTCCCTTTGGTTACAGCTGCTAATTTCTAATGA
GTTTGAACTGCTTCATTATCCCGTTCATAATTATATTGTCATTCTTGTAA
TTGAATCTCATTTAGATGGCTTGAAACTGTAAATAGAATTTCATTTTTTC
TGACTTCGTTAATGTTTTAGCCCCCTTTGCATAATTGCCTCTGAGTTAAC
CCGTCAATTATAAAGTCGTCATCTTTTATTGTAATTCAGGCATATTCTGA
CGATTTTAAGCGACAAATGGAAGTCCATTTCGAAGAAAAACTCAGCGGCT
TTATTACCGAAATGAGAACAGTATTTGAAATGGAATTGAGTCGAGTGCGA
AGTGAATATTCTGGATTAAATCGGAGCCCGATTAGTGAGACAGAGGAGGG
ACGCGATTCGGTCATTGAAAGTGGTGCTATTGCTGATCCGTACATTTGGC
GAATCAACGAGCTGTCTACAATTTACAAAGAATTCGACAGCAGTTTGGAT
TTTTTTTCCCAAGACAAATGCTATTTGTTTCGGATGGTGCTGAATAGGGG
GATGATTGGAACGGAATTCAATGTTGATTTAGTGCTCGTCGATGAAGGTT
GCGAGTCAGGTGATGGCTTCCCCATGAATCGACTGGTGAAAATCAATATT
CTCAACCAGGCAACCAATGCTCCTTTCATTGGTTTCACCAGGAACTGTTC
CATGAATAAAGGTGATACCGAGCGGATTTTTAGATATTCGGTTTCTGACC
TTCCACTGGAGGCCGTTTTAAAAGATGACTCGATCGTTCTAGAATGCATT
ATCTAGATTATATGTTGCTCATTGCCAACCGATTTGATCGTTTTTGTGTG
TATTTTTCATGTTGTAAATTTATATGAATTTCATTGGTCAATTTTTATAT
CCAATAGATCGGAA
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protein sequence of SMED30027566-orf-1

>SMED30027566-orf-1 ID=SMED30027566-orf-1|Name=SMED30027566-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp
MEVHFEEKLSGFITEMRTVFEMELSRVRSEYSGLNRSPISETEEGRDSVI
ESGAIADPYIWRINELSTIYKEFDSSLDFFSQDKCYLFRMVLNRGMIGTE
FNVDLVLVDEGCESGDGFPMNRLVKINILNQATNAPFIGFTRNCSMNKGD
TERIFRYSVSDLPLEAVLKDDSIVLECII*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000420parapharyngeal region
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0003116parenchymal cell