SMED30023515

Overview
NameSMED30023515
Smed IDSMED30023515
Length (bp)781
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 SMED30023515 (SMED30023515) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023515 (SMED30023515) 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 SMED30023515 (SMED30023515) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023515 (SMED30023515) 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




SMED30023515

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023515h1SMcG0020730 dd_Smed_v4_1692_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30023515 vs. Planmine SMEST
Match: SMESG000039477.1 (SMESG000039477.1)

HSP 1 Score: 257.299 bits (656), Expect = 7.982e-85
Identity = 150/158 (94.94%), Postives = 153/158 (96.84%), Query Frame = 1
Query:   67 MEPTKIIEKLKGXXXXXXXXXXXXXXKQKLIKRAKEDISTISNLYSDEHCXXXXXXXXXXXVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITTTMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 540
            MEPTKIIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKL DIDKD+TTERIYE LSMRLEITKFGKSWNKLM K +NIEDEI TTM+EQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP
Sbjct:  186 MEPTKIIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKLSDIDKDITTERIYEILSMRLEITKFGKSWNKLMKKAENIEDEIATTMKEQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 343          
BLAST of SMED30023515 vs. Planmine SMEST
Match: SMESG000065358.1 (SMESG000065358.1)

HSP 1 Score: 260.381 bits (664), Expect = 4.320e-84
Identity = 152/158 (96.20%), Postives = 154/158 (97.47%), Query Frame = 1
Query:   67 MEPTKIIEKLKGXXXXXXXXXXXXXXKQKLIKRAKEDISTISNLYSDEHCXXXXXXXXXXXVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITTTMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 540
            MEPTKIIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKLIDIDKDVTTERIYE L MRLEITKFGKSWNKLM KVKNIEDEI TTM+EQTKAY+ECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP
Sbjct:  343 MEPTKIIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHCILIKLIDIDKDVTTERIYEILFMRLEITKFGKSWNKLMEKVKNIEDEIATTMKEQTKAYVECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 500          
BLAST of SMED30023515 vs. Planmine SMEST
Match: SMESG000029555.1 (SMESG000029555.1)

HSP 1 Score: 197.593 bits (501), Expect = 2.566e-57
Identity = 105/115 (91.30%), Postives = 109/115 (94.78%), Query Frame = 1
Query:  145 KQKLIKRAKEDISTISNLYSDEHCXXXXXXXXXXXVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITTTMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESH 489
            KQKLIKRAKEDIS ISNLYSDEHCILIKLIDIDKDVTTERIYE LSMR+EITKFGKSW KLM KVKNIEDEI TT++EQTKAY+ECY CKTEEARVMVIPCGHLSYCHGCAQESH
Sbjct:  549 KQKLIKRAKEDISAISNLYSDEHCILIKLIDIDKDVTTERIYEILSMRVEITKFGKSWYKLMEKVKNIEDEIATTVKEQTKAYVECYTCKTEEARVMVIPCGHLSYCHGCAQESH 663          
BLAST of SMED30023515 vs. Planmine SMEST
Match: SMESG000029555.1 (SMESG000029555.1)

HSP 1 Score: 197.593 bits (501), Expect = 2.667e-57
Identity = 105/115 (91.30%), Postives = 109/115 (94.78%), Query Frame = 1
Query:  145 KQKLIKRAKEDISTISNLYSDEHCXXXXXXXXXXXVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITTTMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESH 489
            KQKLIKRAKEDIS ISNLYSDEHCILIKLIDIDKDVTTERIYE LSMR+EITKFGKSW KLM KVKNIEDEI TT++EQTKAY+ECY CKTEEARVMVIPCGHLSYCHGCAQESH
Sbjct:  556 KQKLIKRAKEDISAISNLYSDEHCILIKLIDIDKDVTTERIYEILSMRVEITKFGKSWYKLMEKVKNIEDEIATTVKEQTKAYVECYTCKTEEARVMVIPCGHLSYCHGCAQESH 670          
BLAST of SMED30023515 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 189.119 bits (479), Expect = 2.156e-54
Identity = 113/159 (71.07%), Postives = 136/159 (85.53%), Query Frame = 1
Query:   67 MEPTK-IIEKLKGXXXXXXXXXXXXXXKQKLIKRAKEDISTISNLYSDEHCXXXXXXXXXXXVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITTTMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIKERLTVYFP 540
            ME TK II KL+ ILNIENDNLE LINKQKL+++ KED+++IS+LY DE C LIKLI+ID++V TERIYE L MRLEI +FGK W+ +M KV+ IEDEI   M+EQTKAY ECY C+TEEARVMVIPCGHLS+C GCA+ESHC+LCQRKIKER+TV++P
Sbjct: 2490 MEQTKPIITKLREILNIENDNLERLINKQKLMRKVKEDLASISSLYPDELCTLIKLINIDEEVITERIYEILLMRLEIAEFGKEWSIMMEKVETIEDEIMRMMKEQTKAYRECYVCRTEEARVMVIPCGHLSFCQGCAKESHCVLCQRKIKERITVFYP 2648          
The following BLAST results are available for this feature:
BLAST of SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 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 SMED30023515 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039477.17.982e-8594.94SMESG000039477.1[more]
SMESG000065358.14.320e-8496.20SMESG000065358.1[more]
SMESG000029555.12.566e-5791.30SMESG000029555.1[more]
SMESG000029555.12.667e-5791.30SMESG000029555.1[more]
SMESG000052862.12.156e-5471.07SMESG000052862.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023515 ID=SMED30023515|Name=SMED30023515|organism=Schmidtea mediterranea sexual|type=transcript|length=781bp
GAATCTAGTTAATTAGTATTTAAATAAATTTAAAGAGTAATTAAAAGAGA
TTTAATAATTTTAGAAATGGAACCAACAAAAATAATAGAAAAACTAAAAG
GGATCCTAAACATCGAAAATGACAATCTTGAGGAACTAATTAATAAACAA
AAGTTAATTAAACGAGCTAAAGAGGATATATCAACGATTTCCAACCTGTA
TTCCGACGAACATTGCATATTGATAAAATTGATTGACATTGATAAAGACG
TGACAACGGAAAGAATATACGAAACTCTATCTATGAGATTGGAAATAACC
AAATTTGGAAAAAGCTGGAACAAGTTAATGGGAAAAGTCAAAAATATTGA
AGACGAGATTACAACAACAATGAGAGAGCAAACCAAGGCTTATTTGGAAT
GTTATGCGTGCAAAACAGAGGAAGCACGAGTAATGGTGATACCTTGCGGA
CACCTGAGTTATTGTCATGGATGCGCACAAGAGTCGCACTGTATGTTATG
CCAGCGAAAGATAAAGGAAAGACTAACGGTTTACTTTCCATGAATTGTTA
TGATGAAATGAAATAAATGTGTATTATGCATTACTTGAATTATTATTAGA
TGATAAGACGAATATGAAAGAAATATGCAATGTTTGTAAATAATAAAACC
ACCCGACAACGATAAATAAAGGTAATAGACCGAATACATGAAAGCCGAAT
TAGGGAAATAATTAAAACACATGCACAGAGACACAAATATTGGACGGAAA
AATTTCGACAACCGAACTTCCAGATCGGAAG
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protein sequence of SMED30023515-orf-1

>SMED30023515-orf-1 ID=SMED30023515-orf-1|Name=SMED30023515-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MEPTKIIEKLKGILNIENDNLEELINKQKLIKRAKEDISTISNLYSDEHC
ILIKLIDIDKDVTTERIYETLSMRLEITKFGKSWNKLMGKVKNIEDEITT
TMREQTKAYLECYACKTEEARVMVIPCGHLSYCHGCAQESHCMLCQRKIK
ERLTVYFP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding