SMED30021709

Overview
NameSMED30021709
Smed IDSMED30021709
Length (bp)979
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 SMED30021709 (SMED30021709) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021709 (SMED30021709) 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



SMED30021709

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30021709 SmedASXL_064229SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30021709 SmedASXL_064229SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30021709 SmedASXL_064229SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30021709 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.034253:261..4047 +4826
v31.045739:411..2210 +4807
v31.045739:1..936 -4645
v31.045739:1686..2507 -4101
v31.034253:1..785 -3886
v31.002931:63550..64433 +3203
Homology
[Close]
BLAST of SMED30021709 vs. TrEMBL
Match: A0A195D1X8 (Uncharacterized protein OS=Cyphomyrmex costatus OX=456900 GN=ALC62_02112 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 8.165e-7
Identity = 27/44 (61.36%), Postives = 33/44 (75.00%), Query Frame = -2 
Query:  697 NFQFVLYCKKLRAQPGFEPGTTRTLSEYHTPRPLSRHKFAIKFI 828
            NFQ + +  K+ AQPGFEPGT+RT SE HTPRPLSR  + +KF 
Sbjct:   84 NFQEITFGTKIWAQPGFEPGTSRTQSENHTPRPLSR-SWNVKFT 126

HSP 2 Score: 58.151 bits (139), Expect = 8.165e-7
Identity = 27/44 (61.36%), Postives = 33/44 (75.00%), Query Frame = -2 
Query:  244 NFQFVLYCKKLRAQPGFEPGTTRTLSEYHTPRPLSRHKFAIKFI 375
            NFQ + +  K+ AQPGFEPGT+RT SE HTPRPLSR  + +KF 
Sbjct:   84 NFQEITFGTKIWAQPGFEPGTSRTQSENHTPRPLSR-SWNVKFT 126
The following BLAST results are available for this feature:
BLAST of SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A195D1X88.165e-761.36Uncharacterized protein OS=Cyphomyrmex costatus OX... [more]
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BLAST of SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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 SMED30021709 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

>SMED30021709 ID=SMED30021709|Name=SMED30021709|organism=Schmidtea mediterranea sexual|type=transcript|length=979bp
AAACAACAACTACGACAACATGAACAAGTGAGGAGCATAGAAATTTTATC
AAGTTCAACGTTCGATTGAGTTTGTCATCAAAGAAAAAGAGAATTGAGAA
AGCGAAATTAAGATTAGAAAAATCTACTGGATGACAAAAATGCGGACATT
TATTGAATTGAGAAACCGAAAATAGAAAAATCACGTGACAAAACATGAAA
TGGATGATGATTTATTGAAAATAATAAAAAGGGTAAAATTTTTGATAAAT
TTGATGGCAAATTTATGTCGGCTCAGTGGTCTAGGGGTATGATACTCGCT
TAGGGTGCGAGTGGTCCCGGGTTCAAATCCCGGCTGAGCCCTTAATTTTT
TACAGTACAATACAAATTGGAAATTCGATTTTCAACACGAAATTTCTTTC
ATGTCAGCTTTTACTGATGGATAACGGAAAAAAGCTAAAAACGCAAAAGT
CCTAAACAACAACTACGACAACGTGAACAAGTGAGGAGCATAGAAATTTT
ATCAAGTTCAACGTTCGATTGAGTTTGTCATCAAAGAAAAAGAGAATTGA
GAAAGCGAAATTAAGATTAGAAAAATCTACTGGATGACAAAAATGCGGAC
ATTTATTGAATTGAGAAACCGAAAATAGAAAAATCACGTGACAAAACATG
AAATGGATGATGATTTATTGAAAATAATAAAAAGGGTAAAATTTTTGATA
AATTTGATGGCAAATTTATGTCGGCTCAGTGGTCTAGGGGTATGATACTC
GCTTAGGGTGCGAGTGGTCCCGGGTTCAAATCCCGGCTGAGCCCTTAATT
TTTTACAGTACAATACAAATTGGAAATTCGATTTTCAACACGAAATTTCT
TTCATGTCAGCTTTTACTGATGGATAACGGAAAAAAAGCTAAAAACGCAA
AAGTCCTAAACAACAACTACGACAACATGAACAAGTGAGGAGCATAGAAA
TTTTATCAAGTTCAAGGTTCAATTGAGTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002075pigment cell