SMED30028281

Overview
NameSMED30028281
Smed IDSMED30028281
Length (bp)337
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30028281 (SMED30028281) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028281 (SMED30028281) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30028281

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
ciliated epithelial cellSMED30028281 dd_Smed_v4_26410_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
Homology
[Close]
BLAST of SMED30028281 vs. Planmine SMEST
Match: SMESG000079430.1 (SMESG000079430.1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.261e-12
Identity = 26/49 (53.06%), Postives = 37/49 (75.51%), Query Frame = 3 
Query:   45 GKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKLVWIEKHGQNELIH 191
            G  KPKIIKLH+QMF Y N+++ +IVG     LLK VW++KH Q+E+++
Sbjct:  502 GVRKPKIIKLHRQMFIYTNIIDPIIVGDSLVPLLKSVWVDKHDQDEVVN 550
[Close]
BLAST of SMED30028281 vs. Planmine SMEST
Match: SMESG000019334.1 (SMESG000019334.1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.640e-12
Identity = 26/49 (53.06%), Postives = 37/49 (75.51%), Query Frame = 3 
Query:   45 GKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKLVWIEKHGQNELIH 191
            G  KPKIIKLH+QMF Y N+++ +IVG     LLK VW++KH Q+E+++
Sbjct:  237 GVRKPKIIKLHRQMFIYTNIIDPIIVGDSLVPLLKSVWVDKHDQDEVVN 285
[Close]
BLAST of SMED30028281 vs. Planmine SMEST
Match: SMESG000074857.1 (SMESG000074857.1)

HSP 1 Score: 61.2326 bits (147), Expect = 4.893e-12
Identity = 26/49 (53.06%), Postives = 37/49 (75.51%), Query Frame = 3 
Query:   45 GKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKLVWIEKHGQNELIH 191
            G  KPKIIKLH+QMF Y N+++ +IVG     LLK VW++KH Q+E+++
Sbjct:  481 GVRKPKIIKLHRQMFIYTNIIDPIIVGDSLVPLLKSVWVDKHDQDEVVN 529
[Close]
BLAST of SMED30028281 vs. Planmine SMEST
Match: SMESG000042302.1 (SMESG000042302.1)

HSP 1 Score: 61.2326 bits (147), Expect = 5.482e-12
Identity = 26/49 (53.06%), Postives = 37/49 (75.51%), Query Frame = 3 
Query:   45 GKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKLVWIEKHGQNELIH 191
            G  KPKIIKLH+QMF Y N+++ +IVG     LLK VW++KH Q+E+++
Sbjct:  419 GVRKPKIIKLHRQMFIYTNIIDPIIVGDSLVPLLKSVWVDKHDQDEVVN 467
[Close]
BLAST of SMED30028281 vs. Planmine SMEST
Match: SMESG000076652.1 (SMESG000076652.1)

HSP 1 Score: 60.8474 bits (146), Expect = 5.960e-12
Identity = 26/49 (53.06%), Postives = 37/49 (75.51%), Query Frame = 3 
Query:   45 GKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKLVWIEKHGQNELIH 191
            G  KPKIIKLH+QMF Y N+++ +IVG     LLK VW++KH Q+E+++
Sbjct:  241 GVRKPKIIKLHRQMFIYTNIIDPIIVGDSLVPLLKSVWVDKHDQDEVVN 289
The following BLAST results are available for this feature:
BLAST of SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 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 SMED30028281 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079430.14.261e-1253.06SMESG000079430.1[more]
SMESG000019334.14.640e-1253.06SMESG000019334.1[more]
SMESG000074857.14.893e-1253.06SMESG000074857.1[more]
SMESG000042302.15.482e-1253.06SMESG000042302.1[more]
SMESG000076652.15.960e-1253.06SMESG000076652.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028281 ID=SMED30028281|Name=SMED30028281|organism=Schmidtea mediterranea sexual|type=transcript|length=337bp
GACTATCAAAAGAAATATATTTTCAAAATAGTCAAGTTAATGAAGGAAAA
TCAAAACCAAAAATAATTAAACTTCACCAGCAAATGTTCAAATATTGTAA
CATGGTTGAATCTTTAATTGTTGGTCATGTTAACTTTTCGCTTTTGAAAT
TAGTATGGATTGAGAAACACGGACAAAATGAATTAATTCATACCTCACGA
AGGGGCACAGATATATCCATTTCGTCTTTTAAGATGGGTCATATATGTCA
CACTAAATTCATCCGTGTGTTAAACTTCGAAAGATGCGAGAGGATTGATC
TCTTATATCAATCAAGAATTCAATTAGTTAGAGAACC
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protein sequence of SMED30028281-orf-1

>SMED30028281-orf-1 ID=SMED30028281-orf-1|Name=SMED30028281-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=111bp
LSKEIYFQNSQVNEGKSKPKIIKLHQQMFKYCNMVESLIVGHVNFSLLKL
VWIEKHGQNELIHTSRRGTDISISSFKMGHICHTKFIRVLNFERCERIDL
LYQSRIQLVRE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000106ciliated epithelial cell