SMED30008500

Overview
NameSMED30008500
Smed IDSMED30008500
Length (bp)2983
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 SMED30008500 (SMED30008500) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008500 (SMED30008500) 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 SMED30008500 (SMED30008500) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008500 (SMED30008500) 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



SMED30008500

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30008500SMESG000071383.1 dd_Smed_v4_7649_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30008500 dd_Smed_v4_26621_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
[Close]
BLAST of SMED30008500 vs. Planmine SMEST
Match: SMESG000071383.1 (SMESG000071383.1)

HSP 1 Score: 252.677 bits (644), Expect = 7.654e-71
Identity = 147/157 (93.63%), Postives = 149/157 (94.90%), Query Frame = 3 
Query: 2475 FVFSFLYKKWFNQYFMKKYKPPMHKMISNRINVGPLKLNNVDQAAEIIKYEPVXXXXXXXXXXXXXXXXXXXXXXETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERP------KMYADLVIVEQKDKFQIFMSDGSATLNCGV 2927
            F+  FLYKKWFNQYFMKKYKPPMHKMISNRINVGPLKLNNVDQAAEIIKYEPVSYSVSNSSSQIIQQSTSETRISETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERP      +MYADLVIVEQKDKFQIFMSDGSATLNCGV
Sbjct:  664 FIVGFLYKKWFNQYFMKKYKPPMHKMISNRINVGPLKLNNVDQAAEIIKYEPVSYSVSNSSSQIIQQSTSETRISETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERPNNSNLEEMYADLVIVEQKDKFQIFMSDGSATLNCGV 820
[Close]
BLAST of SMED30008500 vs. Planmine SMEST
Match: SMESG000071383.1 (SMESG000071383.1)

HSP 1 Score: 246.128 bits (627), Expect = 1.618e-68
Identity = 147/163 (90.18%), Postives = 149/163 (91.41%), Query Frame = 3 
Query: 2475 FVFSFLYKKWFNQYFMKKYKPPMHKMISNRINVG------PLKLNNVDQAAEIIKYEPVXXXXXXXXXXXXXXXXXXXXXXETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERP------KMYADLVIVEQKDKFQIFMSDGSATLNCGV 2927
            F+  FLYKKWFNQYFMKKYKPPMHKMISNRINVG      PLKLNNVDQAAEIIKYEPVSYSVSNSSSQIIQQSTSETRISETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERP      +MYADLVIVEQKDKFQIFMSDGSATLNCGV
Sbjct:  664 FIVGFLYKKWFNQYFMKKYKPPMHKMISNRINVGKKRNGQPLKLNNVDQAAEIIKYEPVSYSVSNSSSQIIQQSTSETRISETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTDSYTERPNNSNLEEMYADLVIVEQKDKFQIFMSDGSATLNCGV 826
The following BLAST results are available for this feature:
BLAST of SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 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 SMED30008500 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000071383.17.654e-7193.63SMESG000071383.1[more]
SMESG000071383.11.618e-6890.18SMESG000071383.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008500 ID=SMED30008500|Name=SMED30008500|organism=Schmidtea mediterranea sexual|type=transcript|length=2983bp
AATTGACAAATTAAAAACATAATTTTGAACTTATTATATAATTCTTACCT
AAACAAACAAAAAATTAAAAATTCTAAATTTATGAATGAAAACGCACTCA
TTTTATAGATTACTTTATTCTAAATAAATTCTTTCAAGAAAAATTTTCTC
TTTAGTTTTGTTTTTCAACATACCTTAACTTTTCGTTGTTGTTGTGATGA
TGATCCAAAATGGAACAATGCACAAACACAAGAAAAATGAACTACGCAAA
ATAAAAACTTAACTACTGATGAATTAAAAACAATAAAACACAAATAAAAG
GGACCATCTCAATAAATGACGATTTGCAATTTAAAAAAATATTATGTAAA
GATTATGCATCGTAGATCGTTGACATTAATGTTATTTGAAAGATCTTTGC
GATGCGCTTTTAATTAAAAAAACTAAGTTAAAAAATCCTTTATGGTTCAA
AAGTTATGAACCAAGCACCAATTGGTGCTTCCGGTACTCAACTGGTTAAA
ATGTTATTTATGAGATAGACCAGAAAATGTGATTTATAGTTGAAAACTCA
ATGAAGATGAATAAAATTACGAGGATGGATGTTTTAATTATAAATTCAAA
CTTATGACAAATCTTTGGAACCCCACAATATAAGTAATAAATCTATTTAT
TCAAAATAATGCCAAATAATTAAAGCTTTGCATTGAAATTACGAGACATC
CTGCAGTACAATTTTTATTTCAACTAAGTTTTGTGTATTCAAAATTTACA
AATATAACTGCTGTACTTCCTTTACTAGATTTTTACTAGTTATTTATGTT
TTATTCAGTTTTATTTTAAATTTTAAAAATGACATAATAAATTAATATAG
TTAGTTTTAAAAAACGTCTAAGAATTAAGGTTTCATAAGTTATACAATAA
ATTGTACTGTGAGAAAGTTTCGTATAATTTTACGGTAAGTGGTTAACCGC
TTTTTATTGAATACAATTTTGATTTGACCGCTCTACAAATAAACCTAATA
TTAATAAAACCTGCTTGGTTTTAATTCCAGGTTGTTAAATAGAGATGTAG
ATGTACAATAGTTTATTCTCACAAAACTCTCCAACACACTATTACATATA
TAGATCTTCATGGTGTAATGTATTATTTTTCTAATGATATTTAATTTTTT
AATAATTTTTAAATTTAAATGTTTGCCGATTATACAGTTGGAAACAATTG
AAGAGTCTCTGTTAAAAATGTATATGAGATTATCGGGGTGAATTTTATGT
AATATATTGCCAATTTAAGTTTTTATCAAGTTAAATAATAATAAAAAAAA
TAATAACAACATTAGAAAAATTGTAAATAAAAAGCTATATTTAAACCTTG
ATTCTTATTTCTTTAACATGCTTAATGACATTTTACAATTTTAATATTTC
TAACGATAAATTTTATTCTACCATTGACTATAGAGAATTGAATCTTAATT
TTTAAAATTTTATTAAATATTAGTTTAATTAATATTTAAAATAATGTCAC
AAAAAATTCGTTAAACACCAGAAAAATAATAGTAGTAACAAAATGAAACG
TCACACGTATCATTAAAAACAGTTTATTGGTCTACTGATTATTGATACAA
AATACTTTCAAACACACTTACATGCCAACATTCGAAACAATCATCAAACA
TCCTAAACGACCTCTGATCTTAAAAGTACAGTTTTACATATTATTACATA
ATATGTCTAATTAATTCTGTAATATCCATATATCATACTTTCTTACACAT
GTATTAGAATTTTTCTTGCAAAAAAATAATTTTCCATAAAAAATATTATA
ATTCATTGTAATAAAAAAATTTACTAATTTTAGTTGTAAATAATAAAAAA
TCCATTTATCAAAATCTGCATTTAAATTTATTAAAATTAAAATTTTCCTT
TGATAAATGACCTTTCTTAAACTTCTTTGAATAATTAATCGACGTTTGTA
CATTTCCGTGGGTCTTCAAGAATTCAAAACAAAATCTGTTGTTAGTTTTT
GCAGTTTCTGAATTTAAACTGCTATGAACAGAATAATGTTCACGCTATGT
GATGCACATAAACATACTTATTAGATGCATACACAGTCAGAATCTTCCGA
CGAATACGAAATACATTCTGTTAAATCTACAAATAAAAATGAAAGAAGCA
CACTGGTTTTAGTTAATTGCGCTTCTGAGTATTTTTATAACCCGTTGAAA
TTTTTGAAATTTTTAAAATTCTATCGGATAGAGAATAAAAAGTTAGATAG
AATGACTTATAACAAATTTTGGAAATATAAAAATTGAGAAAGTTAAAGGG
GAGGATATGGTGGATGTCTGTACCAGAAAGTTTTTGGTCACCGTAATTGC
CAGTAAGTAAAATATATTATTTTTAAATGCACGAGAAGCCACCATTCAAA
TGGAGTTATTCTTTATTTATAATTTGTTCGGAAAATTGTAATTTAATTTT
TTTATTGTTTCTATTTATTAAACATTTGTTTTTAGTTTCCTATATAAAAA
ATGGTTTAATCAATATTTCATGAAAAAGTATAAACCACCTATGCACAAAA
TGATTTCGAACCGTATTAATGTTGGGCCACTTAAACTCAACAATGTGGAT
CAAGCTGCGGAAATTATAAAATATGAACCGGTTTCGTACTCAGTTTCTAA
TTCTAGCTCCCAAATCATTCAACAAAGTACAAGTGAAACCAGGATTTCAG
AAACCTCTGGCACGTCTGATTACTCCAATACAGATAGTAAAAATAATGAA
ACCGATTTCACAAATAATAGCTACAAACCTCGTCCAGCCCCGAATTGTGG
AATCACAGATTTTACAGACAGTTACACTGAACGGCCAAAAATGTATGCTG
ATTTAGTTATAGTGGAACAAAAAGATAAATTCCAGATTTTTATGTCAGAC
GGGTCTGCAACACTAAACTGCGGTGTTTGAGGCTCATCTGTATATGTAAT
GTAAATAAATTTATTTATGATTTTTGAAAAAAA
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protein sequence of SMED30008500-orf-1

>SMED30008500-orf-1 ID=SMED30008500-orf-1|Name=SMED30008500-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp
MKKYKPPMHKMISNRINVGPLKLNNVDQAAEIIKYEPVSYSVSNSSSQII
QQSTSETRISETSGTSDYSNTDSKNNETDFTNNSYKPRPAPNCGITDFTD
SYTERPKMYADLVIVEQKDKFQIFMSDGSATLNCGV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 40..94
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 40..89