SMED30030681

Overview
NameSMED30030681
Smed IDSMED30030681
Length (bp)732
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 SMED30030681 (SMED30030681) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030681 (SMED30030681) 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 SMED30030681 (SMED30030681) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030681 (SMED30030681) 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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Expression Details

SMED30030681 ( ZPUF-6 ) is expressed during Stage 5, Stage 6, Stage 7 and Stage 8 in the Category 4 cell, epidermis and integumental system

Click to see image symbols and abbreviations
Abbreviation or symbolDefinition
Ooral hemisphere
Aaboral hemisphere
Ddorsal
Vventral
Llateral
black arrowheadembryonic pharynx
red arrowheaddefinitive pharynx
black arrowsprimitive gut
yellow arrowsprimitive ectoderm cells
cyan arrowsbrain
cyan arrowheadsnerve cords
blue arrowheadseye progenitors (trail cells)
purple arrowheadseyes
scale bar100 µm
Anatomical Expression

PAGE et. al., 2020




SMED30030681

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



PAGE Curations: 18

  
PLANA TermReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 4 cellSMED30030681SMESG000038678.1 dd_Smed_v4_327_0_1dd_Smed_v4PMID:28292427whole organismasexual adultsingle-cell RNA-sequencing evidence
epidermisSMED30030681SMESG000038678.1 dd_Smed_v4_327_0_1dd_Smed_v4PMID:28292427whole organismasexual adultsingle-cell RNA-sequencing evidence
epidermal cellSMED30030681SMESG000038678.1 dd_Smed_v4_327_0_1dd_Smed_v4PMID:29674431whole organismasexual adultsingle-cell RNA-sequencing evidence
neoblastSMED30030681SMESG000038678.1 SMED_01590_V2_1rGPL14150_gene_modelsPMID:22385657whole organismasexual adultcDNA to DNA expression microarray evidence
neoblastSMED30030681SMESG000038678.1 SMED_01590_V2_1rGPL14150PMID:22385657whole organismasexual adultcDNA to DNA expression microarray evidence
Category 4 cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 5colorimetric in situ hybridization evidence
epidermal progenitor cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 8colorimetric in situ hybridization evidence
Category 4 cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 7colorimetric in situ hybridization evidence
epidermal progenitor cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 6colorimetric in situ hybridization evidence
epidermal progenitor cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 7colorimetric in situ hybridization evidence
Category 4 cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 6colorimetric in situ hybridization evidence
Category 4 cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 8colorimetric in situ hybridization evidence
epidermal progenitor cellSMED30030681SMESG000038678.1 SMED30030681smed_20140614PMID:28072387whole organismStage 5colorimetric in situ hybridization evidence
headSMED30030681SMESG000038678.1 dd_Smed_v6_327_0_1dd_Smed_v6PMID:28171748whole organismasexual adultRNA-sequencing evidence
head marginSMED30030681SMESG000038678.1 NB.36.10ancbi_smed_estsPMID:25017721whole organismasexual adultcolorimetric in situ hybridization evidence
dorsal ventral margin of the whole animalSMED30030681SMESG000038678.1 NB.36.10ancbi_smed_estsPMID:25017721whole organismasexual adultcolorimetric in situ hybridization evidence
Category 3 cellSMED30030681SMESG000038678.1 dd_Smed_v6_327_0dd_Smed_v6PMID:29674432FACS sorted cell populationasexual adultsingle-cell RNA-sequencing evidence
epidermisSMED30030681SMESG000038678.1 dd_Smed_v6_327_0dd_Smed_v6PMID:29674432FACS sorted cell populationasexual adultsingle-cell RNA-sequencing evidence
Alignments
SMED30030681 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004602:5951..6635 +3081
Homology
BLAST of SMED30030681 vs. Planmine SMEST
Match: SMESG000038678.1 (SMESG000038678.1)

HSP 1 Score: 300.056 bits (767), Expect = 8.985e-105
Identity = 148/148 (100.00%), Postives = 148/148 (100.00%), Query Frame = -2
Query:  144 MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKNIAF 587
            MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKNIAF
Sbjct:    1 MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKNIAF 148          
BLAST of SMED30030681 vs. Planmine SMEST
Match: SMESG000038687.1 (SMESG000038687.1)

HSP 1 Score: 171.785 bits (434), Expect = 2.625e-54
Identity = 83/145 (57.24%), Postives = 107/145 (73.79%), Query Frame = -2
Query:  153 MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKN 587
            MK I+   I   V EC KH+YR YN VTKCDRDWARADRKCDEK+Y+L K+C+++R +FH KYK+ I    C + + + C  EI  +Y  L++G+  IR+WC+ KFE+ID +C KL+ QLH RCD IY RYGKCDRM+VHKI+KN
Sbjct:    1 MKLILIFIICVAVIECKKHDYRSYNLVTKCDRDWARADRKCDEKSYILQKSCHDQRENFHNKYKKTIDKFVCRNEEGD-CIGEISKMYMDLNEGLEKIREWCHGKFELIDEKCGKLSEQLHSRCDIIYNRYGKCDRMRVHKIFKN 144          
BLAST of SMED30030681 vs. Planmine SMEST
Match: SMESG000038673.1 (SMESG000038673.1)

HSP 1 Score: 171.014 bits (432), Expect = 5.808e-54
Identity = 82/145 (56.55%), Postives = 107/145 (73.79%), Query Frame = -2
Query:  153 MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKN 587
            MK I+   I   V EC KH+YR YN VTKCDRDWARADRKCDEK+Y+L K+C+++R +FH KYK+ +    C + + + C  EI  +Y  L++G+  IR+WC+ KFE+ID +C KL+ QLH RCD IY RYGKCDRM+VHKI+KN
Sbjct:    1 MKLILIFIICVAVIECKKHDYRSYNLVTKCDRDWARADRKCDEKSYILQKSCHDQRENFHNKYKKTMDKFVCRNEEGD-CIGEISKMYMDLNEGLEKIREWCHGKFELIDEKCGKLSEQLHSRCDIIYNRYGKCDRMRVHKIFKN 144          
BLAST of SMED30030681 vs. Planmine SMEST
Match: SMESG000024881.1 (SMESG000024881.1)

HSP 1 Score: 44.669 bits (104), Expect = 9.200e-6
Identity = 27/111 (24.32%), Postives = 55/111 (49.55%), Query Frame = -2
Query:  180 TKCDRDWARADRKCDEKAYVLHKACYERRAHFHLKYKEEI--ANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRKWCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDR 506
            T+C+ ++   D+ CD K   L K C  +    +  + +++  AN KC +  T++ R  + +L  ++      + K C  ++  +D  C +   +L   C P+Y++  KC+R
Sbjct:   40 TECEDEYEELDKLCDPKYEALDKQCLPKYVQINADFAKQVVNANLKCQETPTKAGRKVVRDLEKQIFGDYDKLDKTCDPQYAALDKECLEQYQKLDKHCLPLYEQQKKCER 150          
The following BLAST results are available for this feature:
BLAST of SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 vs. UniProt
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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 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 SMED30030681 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000038678.18.985e-105100.00SMESG000038678.1[more]
SMESG000038687.12.625e-5457.24SMESG000038687.1[more]
SMESG000038673.15.808e-5456.55SMESG000038673.1[more]
SMESG000024881.19.200e-624.32SMESG000024881.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030681 ID=SMED30030681|Name=SMED30030681|organism=Schmidtea mediterranea sexual|type=transcript|length=732bp
TATGGATATACATATAATAAAAAGATTCTTCGTTTTTCTCAAGCTTCCAA
GTTATAGTTTCGTAGTTTTAAAAAAAAAATTATTATACCCTATTACTAAA
CAAATAAAATTTTAATTATCTCAAAAACGAAATCCACATTTTAAAAAGCT
ATGTTTTTATAAATTTTGTGCACTTTCATTCGATCACATTTTCCATATCT
CTGATAGATCGGATCGCATCTCAAGTGCAATTGATGTGCTAATTTGTCGC
ATCTGTGATCGATAATTTCGAATTTTCTGTAACACCATTTTCTGATGACC
CGGATACCTTGATCGAGTTTGGCGTACAAATTATCAATCTCTATTCGACA
TGACTCAGTTTGAACGTCAACGCATTTGTGATTTGCGATTTCTTCCTTAT
ATTTCAAATGAAAATGAGCTCGGCGTTCATAACAGGCCTTGTGGAGAACA
TAAGCCTTTTCATCGCATTTCCGATCGGCTCTGGCCCAGTCTCTGTCACA
TTTAGTGACAGCATTGTAGAATCGGTATTCGTGTTTGCTGCACTCAGTAA
CGATAAAAAGAATAGCCAAAAATATTATGTATTTCATTTTCAAAATAAAT
TTTGAAAAAAAAAAAAAAAAAAGATAAATTTACCGTATTCAGCGATATTT
TTCTTTGGCATAGCATACATAATATTTTCCATTTTAAAAATGAAATAAAA
TGAATAAGCAAGTTGTTTTAATCAATCATTAG
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protein sequence of SMED30030681-orf-1

>SMED30030681-orf-1 ID=SMED30030681-orf-1|Name=SMED30030681-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=149bp
MKYIIFLAILFIVTECSKHEYRFYNAVTKCDRDWARADRKCDEKAYVLHK
ACYERRAHFHLKYKEEIANHKCVDVQTESCRIEIDNLYAKLDQGIRVIRK
WCYRKFEIIDHRCDKLAHQLHLRCDPIYQRYGKCDRMKVHKIYKNIAF*
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Aliases
The feature 'SMED30030681' has the following synonyms
Synonym
ZPUF-6
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000033epidermal progenitor cell
PLANA:0000035Category 3 cell
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000418head
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0007561head margin
PLANA:0000034epidermis
PLANA:0000018Category 4 cell
PLANA:0004529integumental system
Vocabulary: Schmidtea mediterranea Developmental Stages
TermDefinition
PLANA:0000005Stage 5
PLANA:0000008Stage 8
PLANA:0000006Stage 6
PLANA:0000007Stage 7