SMED30001271

Overview
NameSMED30001271
Smed IDSMED30001271
Length (bp)1116
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 SMED30001271 (SMED30001271) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001271 (SMED30001271) 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 SMED30001271 (SMED30001271) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001271 (SMED30001271) 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




SMED30001271

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30001271SMESG000038975.1 Contig4799newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30001271SMESG000038975.1 Contig4799uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30001271SMESG000063552.1 Contig4799newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30001271SMESG000063552.1 Contig4799uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001271SMESG000038975.1 dd_Smed_v4_930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001271SMESG000038975.1 Contig4799newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001271SMESG000038975.1 Contig4799uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001271SMESG000063552.1 Contig4799newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001271SMESG000063552.1 Contig4799uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30001271 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000700:106706..107729 -3151
Homology
BLAST of SMED30001271 vs. Planmine SMEST
Match: SMESG000038975.1 (SMESG000038975.1)

HSP 1 Score: 237.269 bits (604), Expect = 3.190e-77
Identity = 198/199 (99.50%), Postives = 198/199 (99.50%), Query Frame = 3
Query:   48 MSWEDEDAAIPTMVANRFAGEDEDATIPDSWDAEEDEPVKKISEPVXXXXXXXXXXXXXXXXXXXXXXTDNVPLTEKERENFEKNAEFELFKDALEIKPIVNGXXXXXXXXXXXXXXXXXXXXXXILPFESHSYYSTFLENTFRDLVISSDVDTLKKFSVMFNALANEXXXXXXXXXXXXXXXXXXXXXXVRVNDVTNY 644
            MSWEDEDAAIPTMVANRFAGEDEDATIPDSWDAEEDEPVKKISEPVKKIEVKSKLLKKELKEKE KKKTDNVPLTEKERENFEKNAEFELFKDALEIKPIVNGIDDIQIKGKDDFDKLKELLKKKILPFESHSYYSTFLENTFRDLVISSDVDTLKKFSVMFNALANEKSKVQKTTGKKKKAIKGAKLATVRVNDVTNY
Sbjct:    1 MSWEDEDAAIPTMVANRFAGEDEDATIPDSWDAEEDEPVKKISEPVKKIEVKSKLLKKELKEKEFKKKTDNVPLTEKERENFEKNAEFELFKDALEIKPIVNGIDDIQIKGKDDFDKLKELLKKKILPFESHSYYSTFLENTFRDLVISSDVDTLKKFSVMFNALANEKSKVQKTTGKKKKAIKGAKLATVRVNDVTNY 199          
The following BLAST results are available for this feature:
BLAST of SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 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 SMED30001271 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000038975.13.190e-7799.50SMESG000038975.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001271 ID=SMED30001271|Name=SMED30001271|organism=Schmidtea mediterranea sexual|type=transcript|length=1116bp
TCACTTTTTTAAATTTCATATAGTCATCGTTGAAATTTTATTGAAAAATG
TCTTGGGAAGATGAAGATGCTGCTATACCGACTATGGTGGCCAATCGTTT
TGCTGGGGAAGATGAAGATGCTACAATACCTGATTCCTGGGATGCTGAAG
AAGATGAACCAGTGAAAAAGATTTCAGAACCTGTAAAAAAGATTGAAGTT
AAATCAAAATTACTGAAAAAAGAACTAAAAGAAAAAGAGTTAAAGAAAAA
AACCGACAATGTTCCACTCACAGAAAAGGAAAGAGAAAATTTTGAGAAAA
ATGCTGAATTTGAATTGTTTAAAGATGCATTAGAAATAAAACCAATTGTA
AATGGTATAGACGATATTCAAATCAAAGGTAAAGATGATTTTGATAAATT
AAAGGAGCTTTTAAAAAAGAAAATTTTACCTTTTGAAAGTCATTCTTATT
ACAGCACATTTTTAGAAAACACTTTTCGTGATTTAGTTATATCCTCTGAT
GTCGACACATTAAAGAAGTTCTCAGTAATGTTCAATGCATTAGCAAATGA
AAAATCAAAAGTGCAAAAAACCACCGGTAAGAAAAAGAAAGCCATTAAAG
GAGCAAAATTAGCAACAGTCAGAGTTAATGACGTAACCAATTACGAGGAC
GACGAAGATTTGGAATTTGATGAAGATTATTGAAAACACACGGTCATTAT
AGTCGTGGAATAAATTCAATTGGCTTTTTGAAATTTTTTGTCAAGTTTAT
CGATGATAAAAAGTTTTTTATTGATTTTATTTTCCGTTTAAAAAATATTT
TTTTGAGTTCCAAATATTTATAGGAACAAATAGACATACTTTTGATCATT
GCTTCGTGGTATTGAACTAGACATTTTGTGTATTGGTCGAATGGATATCA
AAATTTGTATTGAGAATCTTTTTGATTTATGTTACTATTTTTAGTAACAA
GAATTCTAATCGATAATCACGGTGTTGTTGATTAGTAAATGATGTTTTTG
GTTGAATGGTTTGATTACAAATTGTGTTTATGTGATTTCTCAATATCGTA
ACTAGGGCAACCGCGTTATTTTTATAGGTGTGAAATTGGTTAAAAATCAA
TAAAATTCTTTATTCA
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protein sequence of SMED30001271-orf-1

>SMED30001271-orf-1 ID=SMED30001271-orf-1|Name=SMED30001271-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=212bp
MSWEDEDAAIPTMVANRFAGEDEDATIPDSWDAEEDEPVKKISEPVKKIE
VKSKLLKKELKEKELKKKTDNVPLTEKERENFEKNAEFELFKDALEIKPI
VNGIDDIQIKGKDDFDKLKELLKKKILPFESHSYYSTFLENTFRDLVISS
DVDTLKKFSVMFNALANEKSKVQKTTGKKKKAIKGAKLATVRVNDVTNYE
DDEDLEFDEDY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000429neoblast
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR013906eIF3j
IPR023194eIF3-like_dom_sf
Vocabulary: cellular component
TermDefinition
GO:0005852eukaryotic translation initiation factor 3 complex
GO:0005737cytoplasm
GO:0016282eukaryotic 43S preinitiation complex
GO:0033290eukaryotic 48S preinitiation complex
Vocabulary: molecular function
TermDefinition
GO:0003743translation initiation factor activity
Vocabulary: biological process
TermDefinition
GO:0001731formation of translation preinitiation complex
GO:0006412translation
GO:0006413translational initiation
GO:0006446regulation of translational initiation
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013906Eukaryotic translation initiation factor 3 subunit JPFAMPF08597eIF3_subunitcoord: 1..208
e-value: 3.6E-29
score: 102.4
IPR013906Eukaryotic translation initiation factor 3 subunit JPANTHERPTHR21681EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT Jcoord: 1..204
IPR023194Eukaryotic translation initiation factor 3-like domain superfamilyGENE3DG3DSA:1.10.246.60coord: 100..179
e-value: 9.0E-21
score: 75.9
NoneNo IPR availablePANTHERPTHR21681:SF0EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT Jcoord: 1..204