SMED30016055

Overview
NameSMED30016055
Smed IDSMED30016055
Length (bp)1294
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 SMED30016055 (SMED30016055) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016055 (SMED30016055) 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



SMED30016055

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30016055h1SMcG0008266 dd_Smed_v4_4928_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30016055h1SMcG0008266 dd_Smed_v4_4928_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016055h1SMcG0008266 dd_Smed_v4_4928_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30016055h1SMcG0008266 dd_Smed_v4_4928_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016055h1SMcG0008266 dd_Smed_v4_4928_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30016055h1SMcG0008266 dd_Smed_v6_4928_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30016055h1SMcG0008266 dd_Smed_v4_4928_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
SMED30016055 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016770:1208..2533 -6025
v31.017466:11084..12338 -4789
Homology
[Close]
BLAST of SMED30016055 vs. Planmine SMEST
Match: SMESG000076997.1 (SMESG000076997.1)

HSP 1 Score: 179.489 bits (454), Expect = 2.678e-55
Identity = 86/94 (91.49%), Postives = 90/94 (95.74%), Query Frame = 2 
Query:  401 MFTRVFDLKNLAGLRKLEMLEKITYRSKITKTLATFKHPKVCYINSLMKFSKARIVSGRKEKIMNNFLIHIYDLTAATIDSCRLDLTFDDFSLS 682
            MFTRVFDLKNLA LRKLEMLEKITYRSK+TKTLATFKHPKVCYINSLMKFSKARI+SGRKEKIMNNFLIHI+DLT A I SCRLDLTFDDFSL+
Sbjct:    1 MFTRVFDLKNLAALRKLEMLEKITYRSKVTKTLATFKHPKVCYINSLMKFSKARIISGRKEKIMNNFLIHIHDLTVAIIVSCRLDLTFDDFSLT 94

HSP 2 Score: 45.4394 bits (106), Expect = 5.887e-6
Identity = 22/23 (95.65%), Postives = 22/23 (95.65%), Query Frame = 1 
Query:  676 SLTTTEEIS*LVQVICCNLSWIF 744
            SLTTTEEIS LVQVICCNLSWIF
Sbjct:   92 SLTTTEEISLLVQVICCNLSWIF 114
The following BLAST results are available for this feature:
BLAST of SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 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 SMED30016055 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000076997.12.678e-5591.49SMESG000076997.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016055 ID=SMED30016055|Name=SMED30016055|organism=Schmidtea mediterranea sexual|type=transcript|length=1294bp
ATAATGTTAACATATAACGTGTGAACATCGACCTAACCGATAAACCATAA
ATCAGAACACGGGACCATGTGCTGCAAATATGAGTCATAGATCAATACTT
GATGGAAATGAATTTTCTGTAAACTTTACTGAAAAATTACAGTGATCCGC
ATGTGTTGTGCCCAATAAGTACTTAGGCTCGACAAAAAATAATTACTTCA
TAAAATATGTATCGCAACCGAGAATACCTAATTATGTATAGTTAATGAAA
AGTTGTTTTTCTAAGCAATTAATTTTTCGAACAAATTGCGCTTTTTCATT
ATTGCCTCTGAAACCTCCATATAATGTTGAATTTTGAAACGTTATAAAGG
TTCAGCATTTAAAGAAAACTTTAACCGAAAGGTTATTGCACAACTATAGG
ATGTTTACAAGAGTTTTTGATTTGAAAAACCTAGCAGGCCTGAGAAAATT
GGAAATGCTGGAGAAAATCACATACCGTAGCAAAATAACTAAAACCTTGG
CAACGTTTAAACATCCCAAAGTATGTTACATAAATTCCTTAATGAAATTT
AGCAAAGCAAGAATAGTCAGCGGTAGAAAAGAGAAAATAATGAACAATTT
CCTAATTCATATATACGACCTGACAGCGGCAACAATTGACTCTTGTCGAC
TCGATCTCACTTTTGATGATTTTAGTCTCTCACAACAACTGAAGAAATTT
CTTAACTTGTTCAAGTAATTTGCTGCAATTTGTCTTGGATTTTCTGATTA
CATCCCCAAGACATTCTTTGAAAATACATTTTGGGCTTGTTAACACGGAT
GGGAAATTGTTTGGAAGATTGGCTAACTTACAGTGAGAAATAAACCTTTT
CAATTGCTTGTTGTTTAAAGTTTGAACAAAATTCGTTACTTATTTCTCGT
CGCGTCTAAGTACTTATTGAATCCACCTTATACTTTTGGTATGATTAGGA
AAATCGTGTAGCTCTTATCTAAGGTGACAAATTCCGATATTGCGAAGAGG
TGTTTCAATTATACATTATTTATTGGAGGAAGCTTTACAAAATATTTACT
CTTGATAAGATTCTAGTGATTTTATATTGTAACCCTCCCTTGTCCGTAAT
ATAGTCATCCATATCCTATAGTTGAAATCATTTTGTGAAAACAATAACTT
TTTGCCATATAATTTAGGTCTGTGAAGTTGTAAGTAAATTTTAGAAATGT
TACCTTAACCATGTTCCCGTTTACGTTTATCAGAAATATGATGTATTTTC
TAATCAATATTTATTTATCAGAGCAACAATGAAAATATATCTGA
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protein sequence of SMED30016055-orf-1

>SMED30016055-orf-1 ID=SMED30016055-orf-1|Name=SMED30016055-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
MFTRVFDLKNLAGLRKLEMLEKITYRSKITKTLATFKHPKVCYINSLMKF
SKARIVSGRKEKIMNNFLIHIYDLTAATIDSCRLDLTFDDFSLSQQLKKF
LNLFK*
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