SMED30003429

Overview
NameSMED30003429
Smed IDSMED30003429
Length (bp)898
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 SMED30003429 (SMED30003429) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003429 (SMED30003429) 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 SMED30003429 (SMED30003429) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003429 (SMED30003429) 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



SMED30003429

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



PAGE Curations: 27

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30003429h1SMcG0023080 SmedASXL_018632SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig34357uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig34357newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig28971uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig28971newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig12708newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig12708uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig46250newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig46250uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig50537uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003429h1SMcG0023080 Contig50537newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30003429h1SMcG0023080 dd_Smed_v4_4433_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30003429h1SMcG0023080 dd_Smed_v4_5235_0_7dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30003429h1SMcG0023080 dd_Smed_v4_5235_0_7dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30003429h1SMcG0023080 dd_Smed_v4_990_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30003429h1SMcG0023080 dd_Smed_v6_5235_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30003429h1SMcG0023080 dd_Smed_v6_990_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
musculature systemSMED30003429h1SMcG0023080 dd_Smed_v6_990_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle progenitor cellSMED30003429h1SMcG0023080 dd_Smed_v6_990_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003429h1SMcG0023080 dd_Smed_v4_4433_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30003429h1SMcG0023080 dd_Smed_v4_4433_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
SMED30003429 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000150:118321..119272 +4400
Homology
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BLAST of SMED30003429 vs. Planmine SMEST
Match: SMESG000007226.1 (SMESG000007226.1)

HSP 1 Score: 219.164 bits (557), Expect = 1.616e-72
Identity = 111/112 (99.11%), Postives = 111/112 (99.11%), Query Frame = 2 
Query:  380 MFSKLLLFFVIVLSNSPCNLAQLTCYMCDPCDNPFVPKPSLTAASCAFCSVYNNGSYFARKCSNLCINGFYNGLNTQCCNSNYCNSKNQLTSTSGLYLTISCFTLAIIYSMK 715
            MFSKLLLFFVIVLSNSPCNLAQLTCYMCDPCDNPFVPKP LTAASCAFCSVYNNGSYFARKCSNLCINGFYNGLNTQCCNSNYCNSKNQLTSTSGLYLTISCFTLAIIYSMK
Sbjct:    1 MFSKLLLFFVIVLSNSPCNLAQLTCYMCDPCDNPFVPKPPLTAASCAFCSVYNNGSYFARKCSNLCINGFYNGLNTQCCNSNYCNSKNQLTSTSGLYLTISCFTLAIIYSMK 112
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BLAST of SMED30003429 vs. Planmine SMEST
Match: SMESG000007247.1 (SMESG000007247.1)

HSP 1 Score: 47.7506 bits (112), Expect = 2.150e-7
Identity = 24/63 (38.10%), Postives = 37/63 (58.73%), Query Frame = 2 
Query:  380 MFSKLLLFFVIVLSNSPCNLAQLT-CYMCDPCDNPFVPKPSLTAASCAFCSVYNNGSYFARKC 565
            M SKLLLFFVI +++     AQL  CY+C  C NPF+   ++T+ +C+ C      +  ++ C
Sbjct:    1 MISKLLLFFVIAITDLQLGHAQLINCYVCAGCPNPFIISGAMTSTNCSSCMTTTALTVISKTC 63
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BLAST of SMED30003429 vs. Planmine SMEST
Match: SMESG000031270.1 (SMESG000031270.1)

HSP 1 Score: 48.521 bits (114), Expect = 3.864e-7
Identity = 34/93 (36.56%), Postives = 52/93 (55.91%), Query Frame = 2 
Query:  380 MFSKLLLFFVIVLSNSPCNLAQLT-CYMCDPCDNPFVPKPSLTAASCAFCSVYNNG-SYFARKCSNLCINGF--YNGLNTQCCNSNYCNSKNQ 646
            M SKLLLFFVI +++      QL  CY C  C NPFV   +LTA +C+ C+   +  +   + C+++  N    Y G    CC++N CN+ ++
Sbjct:    1 MISKLLLFFVIAITDLQLGHTQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSYIGATNICCSTNLCNTGSE 93
The following BLAST results are available for this feature:
BLAST of SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 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 SMED30003429 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000007226.11.616e-7299.11SMESG000007226.1[more]
SMESG000007247.12.150e-738.10SMESG000007247.1[more]
SMESG000031270.13.864e-736.56SMESG000031270.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003429 ID=SMED30003429|Name=SMED30003429|organism=Schmidtea mediterranea sexual|type=transcript|length=898bp
AAAAAAACAGCTTTGGAGTATATTCATAACTCATTCAAAATTTCCTTCTA
AGACTTCCAAAACCAACCAATCATTCACTAGAGCTGATGCACAACCGCGA
TGACGTAATTTCAACACCAATCAAAACTTCTATAATAAATGAGAAAATCT
TTAAAAAAAAATCAAATCACATTTGGACTCATTCATTGACCACAGCAATT
GTTATGGACAATTTCAAAGGACAAAAATAAATTTATCGGCCATTTTGATT
TCATTGATTATTAGAGTATTGTAAGATCAACTCGCGCATCACGCACTGCA
GAAATGCTATTACAACAATAGCCGTCATTAAATCAGCATTTAATCAATTA
ACTTGAATTAAATCATCAATCGAAAGAGAATGTTTAGTAAATTGCTTCTC
TTTTTCGTTATTGTTTTATCAAATTCGCCGTGCAACTTGGCCCAACTGAC
CTGCTATATGTGTGACCCATGTGACAATCCATTTGTTCCTAAGCCATCAT
TAACGGCAGCCAGTTGTGCTTTCTGTTCGGTCTATAACAATGGATCTTAT
TTTGCTAGAAAATGTTCTAATTTATGCATTAATGGATTTTACAATGGTCT
GAATACTCAATGCTGTAATAGTAATTACTGTAACTCCAAAAACCAACTGA
CAAGTACTTCTGGATTATATCTAACTATTTCCTGTTTCACCCTGGCGATT
ATTTATTCAATGAAATAATTTATTTTGTTTTAATCTATTCTATGTGAAAC
TCAAACATTTCGAATTATGAATTATTTTATGAAAATTATTGTATATATTA
TTTATTTTGTAATGCAATTTATTTTCAATTTAGTTTACATGTTAATTCAT
TTTCAATTATTATTTCATTAAATTTTCCGAGTCTAATTGTAAAAGTGC
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protein sequence of SMED30003429-orf-1

>SMED30003429-orf-1 ID=SMED30003429-orf-1|Name=SMED30003429-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MFSKLLLFFVIVLSNSPCNLAQLTCYMCDPCDNPFVPKPSLTAASCAFCS
VYNNGSYFARKCSNLCINGFYNGLNTQCCNSNYCNSKNQLTSTSGLYLTI
SCFTLAIIYSMK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.881