SMED30026041

Overview
NameSMED30026041
Smed IDSMED30026041
Length (bp)1664
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 SMED30026041 (SMED30026041) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026041 (SMED30026041) 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



SMED30026041

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
Category 3 cellSMED30026041 dd_Smed_v4_16497_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
SMED30026041 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001658:16736..18386 +7588
Homology
The following BLAST results are available for this feature:
BLAST of SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 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 SMED30026041 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026041 ID=SMED30026041|Name=SMED30026041|organism=Schmidtea mediterranea sexual|type=transcript|length=1664bp
TTTTAATCCAATTTATATATTGCGACTTATCCAATTCTTCAAAACGTTCA
TCATTCAATTCAATTGATTTGCTTAGAGCCATTTTTTTATATTCAGGAAA
AGGTAGTCTCAATGTCTCAATTATTTGGACTATTGAAGACGATGGCCAAT
TTCGTGATATAACTCGAATAATTTTGCTCTCTGATACATATTATCTTGAT
AAAAATGACAATTTTCTCGACAAATTTTATAGGTCCATCATTGTAGAATT
CAAACGTCCCTGTAAAACAATACCAATTAGTAATATGTATTTTTACAAAA
AATCAATTAAAATCATTTTGAGAACAACTTGTAAATTGCTTCCATAGCCT
TTTCCAATGAGTGACCAGTTTGACTATTTTTAATGCTATTCGCAACAAAT
CAAATTTGGCCACTTGTGCTTAAACGTCTTCAGAATTAACTTGAATTTTG
TTGAAATAGCTCCAAATGATCATAGAATTGTCCGAAAATGCGACCGCCAT
TTAGCCAACAGTTTCAGTTGCAATTTCTATTATAAAATATTATATGCGTT
ATATTTGAAATGTTAAATCACTATAATCAGTTTTTTCAATCATTTCCTAA
GGTAAAACTTCAAAAGGGACTTGCATCTTGGTCACATCAAAATTTGCAAT
CGGATAATAATATCTATAAGGTTTGGTTTTAATTTTTATGACAGTTTTAT
TATTTAAAAATTTAAAGTTGACTCTTGAGTACTCGCGGTAAAAATCACCA
TCTCAGTATTCGTGTTGGGTGAAATAGACAATATGCACTTAATAGCCTAA
AATGATTTTATTTTCAGAATATTTTTTTAAACTCATTAGAGATGATTATA
ATTTCAATAGAAAAAATACAAACCATTAAAGATTTGAAATGATTAAAAGA
AATTTTGTTAAAATTTGTAATGCTAAAAAAAATTCAAATCTTTTAATTTT
ATCAATTACAAGGAATAAAATTAAAGAGCATTGTAGAACGAAGCTATTAG
TAGAAAGTTATTTGAAATAGATCTAGCTTGATTCGCGAGATGTGTGGTGA
TTACACAAATAATGTAAATAAATAAATGATCAATGAAAATTAGAAATTAA
TTAAAAGCTAATTGAATATTCAAAAATGTAAAAATTATTATTTTTCACAG
GAAAAGTGGTACTCGTTGATAAATTAAAAGTTACTATTTAAACTAACTTT
ATATGACGGAAGTTATCTAGGTGGGTCTGAAATGATTTATAAATTGTTAC
CATTTATTATTCAAGGAAATCATTTCATTGGAAAATATTGAAAAGGATAG
ATTGAGTAGTCATTTAAATCATTTAGAAGAAACTGTCCTAACAGTCGTAT
TGACTCTTTGAAAGTGGACATGACAGTGTTCTTAAAATAAATACTTGACT
GAGTAGTAGCTGAAGTTATAAATATTATATTATCAGAATTCAACTTTATA
ATAATAAATTTTATTAATACACCAAAAAGATTAACTGTCACATCTATTTG
ATGTTTTGTAAACAACTGTTCAGGAGTCGTCACATAATAAAAATAACGTC
CATAACAAGGTAGTCGTGATATCTCTTGGATTTACACAAATTTATCTATA
ATACCTCTCATGTAAATTAATTATGATGATTTTTGTTTATCTTGTTAGAT
ACTATCAGTTAAGT
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protein sequence of SMED30026041-orf-1

>SMED30026041-orf-1 ID=SMED30026041-orf-1|Name=SMED30026041-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
LIQFIYCDLSNSSKRSSFNSIDLLRAIFLYSGKGSLNVSIIWTIEDDGQF
RDITRIILLSDTYYLDKNDNFLDKFYRSIIVEFKRPCKTIPISNMYFYKK
SIKIILRTTCKLLP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
Vocabulary: INTERPRO
TermDefinition
IPR013136WSTF_Acf1_Cbp146