SMED30004922

Overview
NameSMED30004922
Smed IDSMED30004922
Length (bp)405
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 SMED30004922 (SMED30004922) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004922 (SMED30004922) 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 SMED30004922 (SMED30004922) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004922 (SMED30004922) 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




SMED30004922

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30004922SMESG000027736.1 SMESG000021798.1 dd_Smed_v4_13_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30004922SMESG000027736.1 SMESG000021798.1 dd_Smed_v6_13_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30004922SMESG000027736.1 SMESG000021798.1 OX_Smed_1.0.21030ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
dorsal-ventral muscle cellSMED30004922SMESG000027736.1 SMESG000021798.1 dd_Smed_v4_13_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004922 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.028149:6685..7029 -1662
v31.007777:36452..36796 -1662
v31.003712:2340..2688 +1560
v31.024411:1932..2278 -1550
v31.007618:37601..37949 +1136
Homology
BLAST of SMED30004922 vs. Planmine SMEST
Match: SMESG000021798.1 (SMESG000021798.1)

HSP 1 Score: 171.014 bits (432), Expect = 1.851e-56
Identity = 85/86 (98.84%), Postives = 85/86 (98.84%), Query Frame = 2
Query:   68 MKSFIVLFTLIIVAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 325
            MKSFIVLFTLII AMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT
Sbjct:    1 MKSFIVLFTLIIAAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 86          
BLAST of SMED30004922 vs. Planmine SMEST
Match: SMESG000027736.1 (SMESG000027736.1)

HSP 1 Score: 171.014 bits (432), Expect = 1.872e-56
Identity = 85/86 (98.84%), Postives = 85/86 (98.84%), Query Frame = 2
Query:   68 MKSFIVLFTLIIVAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 325
            MKSF VLFTLIIVAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT
Sbjct:    1 MKSFFVLFTLIIVAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 86          
BLAST of SMED30004922 vs. Planmine SMEST
Match: SMESG000067669.1 (SMESG000067669.1)

HSP 1 Score: 132.109 bits (331), Expect = 3.086e-41
Identity = 65/72 (90.28%), Postives = 69/72 (95.83%), Query Frame = 2
Query:  110 MCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 325
            MCDEEC D+GS+CAGKTGEACISPDVYENCKKTCHLC DCDDSRPDCG+ KE+GDCDKIDDRICRKTCGVCT
Sbjct:    1 MCDEECADTGSECAGKTGEACISPDVYENCKKTCHLCVDCDDSRPDCGFVKERGDCDKIDDRICRKTCGVCT 72          
BLAST of SMED30004922 vs. Planmine SMEST
Match: SMESG000067662.1 (SMESG000067662.1)

HSP 1 Score: 132.109 bits (331), Expect = 3.086e-41
Identity = 65/72 (90.28%), Postives = 69/72 (95.83%), Query Frame = 2
Query:  110 MCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVCT 325
            MCDEEC D+GS+CAGKTGEACISPDVYENCKKTCHLC DCDDSRPDCG+ KE+GDCDKIDDRICRKTCGVCT
Sbjct:    1 MCDEECADTGSECAGKTGEACISPDVYENCKKTCHLCVDCDDSRPDCGFVKERGDCDKIDDRICRKTCGVCT 72          
BLAST of SMED30004922 vs. Planmine SMEST
Match: SMESG000067659.1 (SMESG000067659.1)

HSP 1 Score: 116.316 bits (290), Expect = 6.154e-35
Identity = 57/85 (67.06%), Postives = 66/85 (77.65%), Query Frame = 2
Query:   68 MKSFIVLFTLIIVAMCDEECVDSGSDCAGKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRICRKTCGVC 322
            MK FI    LI+VAMC E+C+DSG DCA KTGE C + DVY  C K+CH CGDC DSRPDC + KE+GDCDK+DDR+CRKTCG C
Sbjct:    1 MKLFIFFLGLIVVAMC-EDCLDSGDDCASKTGEDCTNEDVYTKCPKSCHFCGDCADSRPDCAFLKERGDCDKMDDRVCRKTCGGC 84          
The following BLAST results are available for this feature:
BLAST of SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 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 SMED30004922 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021798.11.851e-5698.84SMESG000021798.1[more]
SMESG000027736.11.872e-5698.84SMESG000027736.1[more]
SMESG000067669.13.086e-4190.28SMESG000067669.1[more]
SMESG000067662.13.086e-4190.28SMESG000067662.1[more]
SMESG000067659.16.154e-3567.06SMESG000067659.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004922 ID=SMED30004922|Name=SMED30004922|organism=Schmidtea mediterranea sexual|type=transcript|length=405bp
GAATCAGTGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATC
CACGGAAGGCAGCAGACATGAAATCATTCATTGTTTTATTTACTCTCATA
ATTGTTGCAATGTGCGACGAGGAATGTGTGGACTCAGGATCGGACTGTGC
TGGTAAAACTGGCGAAGCTTGTATCAGTCCTGATGTATATGAAAACTGTA
AGAAAACTTGTCATTTATGCGGAGATTGCGACGACAGCAGACCTGACTGC
GGATATGCTAAAGAACAAGGAGATTGTGACAAAATCGATGACAGAATCTG
CAGAAAAACTTGTGGAGTCTGCACTTAAAACTATAATAAAAATTCTAATT
TGAATACGTTTTCTGCTTTTGACAGTAAAATATATTAAAATAAATATTTA
TAGTA
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protein sequence of SMED30004922-orf-1

>SMED30004922-orf-1 ID=SMED30004922-orf-1|Name=SMED30004922-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
NQCSIPEREPEKRLPHPRKAADMKSFIVLFTLIIVAMCDEECVDSGSDCA
GKTGEACISPDVYENCKKTCHLCGDCDDSRPDCGYAKEQGDCDKIDDRIC
RKTCGVCT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002028dorsal-ventral muscle cell
Vocabulary: INTERPRO
TermDefinition
IPR003582ShKT_dom
Vocabulary: molecular function
TermDefinition
GO:0004222metalloendopeptidase activity
GO:0008233peptidase activity
GO:0008237metallopeptidase activity
GO:0008270zinc ion binding
GO:0016787hydrolase activity
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0006508proteolysis