SMED30001824

Overview
NameSMED30001824
Smed IDSMED30001824
Length (bp)872
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 SMED30001824 (SMED30001824) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001824 (SMED30001824) 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 SMED30001824 (SMED30001824) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001824 (SMED30001824) 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




SMED30001824

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30001824h1SMcG0019221 Contig45464uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30001824h1SMcG0019221 Contig45464newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30001824h1SMcG0019221 dd_Smed_v4_2027_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30001824h1SMcG0019221 dd_Smed_v6_2027_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30001824h1SMcG0019221 dd_Smed_v6_2027_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30001824h1SMcG0019221 dd_Smed_v4_2027_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
SMED30001824 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001970:41860..42837 -4297
Homology
BLAST of SMED30001824 vs. Planmine SMEST
Match: SMESG000026020.1 (SMESG000026020.1)

HSP 1 Score: 192.971 bits (489), Expect = 2.916e-62
Identity = 124/124 (100.00%), Postives = 124/124 (100.00%), Query Frame = 1
Query:  136 MFIIYDXXXXXXXXXXXXXXXXXXXXXXXPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS 507
            MFIIYDFVFLFVVMFVLLCLKCKKKELMLPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS
Sbjct:    1 MFIIYDFVFLFVVMFVLLCLKCKKKELMLPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS 124          
BLAST of SMED30001824 vs. Planmine SMEST
Match: SMESG000026020.1 (SMESG000026020.1)

HSP 1 Score: 191.045 bits (484), Expect = 2.088e-61
Identity = 122/125 (97.60%), Postives = 123/125 (98.40%), Query Frame = 1
Query:  136 MFIIYDXXXXXXXXX-XXXXXXXXXXXXXXPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS 507
            MFIIYDFVFLFVV+  VLLCLKCKKKELMLPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS
Sbjct:    1 MFIIYDFVFLFVVVMFVLLCLKCKKKELMLPDEDERENLKEYNESAGETDNNNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFEGTGSQMDDASLIGSLSSYSTETDS 125          
The following BLAST results are available for this feature:
BLAST of SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 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 SMED30001824 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000026020.12.916e-62100.00SMESG000026020.1[more]
SMESG000026020.12.088e-6197.60SMESG000026020.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001824 ID=SMED30001824|Name=SMED30001824|organism=Schmidtea mediterranea sexual|type=transcript|length=872bp
ATCTGATTGGCTAGAAATATTTTATAAGCATACTGCTGTAACTATTATTT
GTAGATTATAATCACAATTATTCCTGTTTAACAAAACTTACACGATTGTT
CTGGTTTGTTACAGTATGTGAATTTATTATTTGTAATGTTCATAATTTAC
GATTTTGTATTTCTATTCGTTGTTATGTTTGTGCTTTTATGTTTGAAATG
CAAAAAGAAAGAATTAATGTTGCCAGATGAAGATGAGCGGGAGAATTTAA
AGGAATATAATGAATCTGCTGGTGAAACAGACAACAATAATTATGATTTA
GCTAAATTGGTTCCGGATTTGGCATTCAGTAATTTGAGTTATAAATTGGA
TCCATTTTTATTAAATGAAAAAAAACAAATTGAAAATGACGAAGGAGGAT
TTCCAATTGATTATCCCTTAGATTACGGTTTTGAAGGTACTGGTAGCCAG
ATGGACGATGCCAGCTTAATAGGATCTTTGAGCAGCTATTCCACAGAAAC
TGATTCATAAAATTAATCACATTCTTCGTGTCTTTTCTTGCCAACTGAGT
TGAAAGCTTTTTTCCTCTCAAATTATCAAACTTTTTATGTTTTTATTTCT
TAAATTTTAATAGTTTTTAAGATTAATTTTAAGCTATTTGCTATTCAGTT
TTGATTGATATTTCCAAGAGTGACATGACAAATACAATAGAAAATAGATT
ATGTAACTTTGAATATTAATAATGCATCGGCGGGTTATATAATGATATTG
AAACAAATTTTGAATTTATAATCATGTCTGTCAATAAAACAAAATAAAAC
CGCAACGTAATATATAAAATATTTCTAAAATATTTTTGATGGTAAAAAAT
ACTTTATTCATTTGGAAATGGA
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protein sequence of SMED30001824-orf-1

>SMED30001824-orf-1 ID=SMED30001824-orf-1|Name=SMED30001824-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MFIIYDFVFLFVVMFVLLCLKCKKKELMLPDEDERENLKEYNESAGETDN
NNYDLAKLVPDLAFSNLSYKLDPFLLNEKKQIENDEGGFPIDYPLDYGFE
GTGSQMDDASLIGSLSSYSTETDS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000035Category 3 cell
PLANA:0000099neuron
PLANA:0000484secretory system
PLANA:0002032epidermal cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR000233Cadherin_cytoplasmic-dom
IPR027397Catenin_binding_dom_sf
Vocabulary: biological process
TermDefinition
GO:0007156homophilic cell adhesion via plasma membrane adhesion molecules
Vocabulary: molecular function
TermDefinition
GO:0005509calcium ion binding
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000233Cadherin, cytoplasmic domainPFAMPF01049Cadherin_Ccoord: 23..119
e-value: 6.9E-10
score: 39.4
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..24
score: 0.71
NoneNo IPR availableTMHMMTMhelixcoord: 4..20