SMED30024073

Overview
NameSMED30024073
Smed IDSMED30024073
Length (bp)651
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 SMED30024073 (SMED30024073) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024073 (SMED30024073) 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 SMED30024073 (SMED30024073) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024073 (SMED30024073) 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



SMED30024073

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
X1 cellSMED30024073SMESG000020681.1 SMESG000020680.1 SmedASXL_010329SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30024073SMESG000020680.1 SmedASXL_069062SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024073 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.021903:478..5591 +1639
v31.022181:1367..6362 +1637
Homology
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BLAST of SMED30024073 vs. TrEMBL
Match: A0A4T0FHX3 (Chromatin modification-related protein OS=Wallemia hederae OX=1540922 GN=E3P99_03014 PE=3 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 5.869e-6
Identity = 21/40 (52.50%), Postives = 24/40 (60.00%), Query Frame = 2 
Query:  458 CICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIWL 577
            C C+   YGNMI C N DC  +WFH  CV IKP   D+W 
Sbjct:  214 CYCQKKSYGNMIGCENDDCPIQWFHFGCVNIKPPEPDVWF 253
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BLAST of SMED30024073 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000000234.1 (pep scaffold:Pmarinus_7.0:GL482739:14:2848:1 gene:ENSPMAG00000000213.1 transcript:ENSPMAT00000000234.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 43.8986 bits (102), Expect = 4.013e-6
Identity = 18/46 (39.13%), Postives = 22/46 (47.83%), Query Frame = 2 
Query:  437 NEREKDVCICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIW 574
            +  E   CIC    YG M+ C N+DC   WFH  CV +K      W
Sbjct:   80 DPNEPRYCICNQVSYGEMVGCDNQDCPIEWFHYGCVGLKEAPKGKW 125
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BLAST of SMED30024073 vs. Ensembl Yeast
Match: YNG1 (Subunit of the NuA3 histone acetyltransferase complex; this complex acetylates histone H3; contains PHD finger domain that interacts with methylated histone H3; shares significant sequence identity with the human candidate tumor suppressor p33-ING1 in C-terminal region [Source:SGD;Acc:S000005590])

HSP 1 Score: 44.2838 bits (103), Expect = 4.136e-6
Identity = 18/46 (39.13%), Postives = 23/46 (50.00%), Query Frame = 2 
Query:  437 NEREKDVCICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIW 574
            N +E+  C CR+  YG M+ C N  C   WFH  CV +K      W
Sbjct:  151 NNQEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKW 196
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BLAST of SMED30024073 vs. Planmine SMEST
Match: SMESG000020680.1 (SMESG000020680.1)

HSP 1 Score: 300.056 bits (767), Expect = 8.906e-105
Identity = 167/168 (99.40%), Postives = 168/168 (100.00%), Query Frame = 2 
Query:   74 MTEHFXXXXXXXLQKFTNDFNLLSHEIQLKDQLVQSLQKEYKETLKSTLANCSXXXXXXXXXXXXQNLIDEKVECSERLCSLVDDCFKQCAEDSSFILKYYSARLMLKKMIPEVYSYSDYVNEREKDVCICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIWL 577
            MTEHFKIKIKKKLQKFTNDFNLLSHEIQLKDQLVQSLQKEYKETLKSTLANCSNIKN+EKIIVKIQNLIDEKVECSERLCSLVDDCFKQCAEDSSFILKYYSARLMLKKMIPEVYSYSDYVNEREKDVCICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIWL
Sbjct:    1 MTEHFKIKIKKKLQKFTNDFNLLSHEIQLKDQLVQSLQKEYKETLKSTLANCSNIKNIEKIIVKIQNLIDEKVECSERLCSLVDDCFKQCAEDSSFILKYYSARLMLKKMIPEVYSYSDYVNEREKDVCICRDSVYGNMIECINKDCATRWFHAHCVKIKPEFADIWL 168
The following BLAST results are available for this feature:
BLAST of SMED30024073 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 SMED30024073 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 SMED30024073 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 SMED30024073 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 SMED30024073 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 SMED30024073 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 SMED30024073 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 SMED30024073 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A4T0FHX35.869e-652.50Chromatin modification-related protein OS=Wallemia... [more]
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BLAST of SMED30024073 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 SMED30024073 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSPMAT00000000234.14.013e-639.13pep scaffold:Pmarinus_7.0:GL482739:14:2848:1 gene:... [more]
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BLAST of SMED30024073 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
YNG14.136e-639.13Subunit of the NuA3 histone acetyltransferase comp... [more]
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BLAST of SMED30024073 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 SMED30024073 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 SMED30024073 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000020680.18.906e-10599.40SMESG000020680.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024073 ID=SMED30024073|Name=SMED30024073|organism=Schmidtea mediterranea sexual|type=transcript|length=651bp
ATTTAATATTATCTTAACGAACGTTTACATTTTATATAATTATTTCACAT
GATTTACAGATTGTCTTTATCTTATGACTGAGCATTTTAAAATAAAAATA
AAAAAAAAATTACAAAAATTCACAAACGATTTCAATCTTTTAAGTCATGA
AATTCAATTGAAAGATCAGCTTGTGCAATCTTTGCAAAAGGAGTACAAGG
AAACTCTAAAATCCACTCTTGCCAATTGTTCAAATATTAAAAATGTAGAA
AAAATTATAGTTAAGATTCAGAATTTAATAGACGAAAAAGTAGAATGCAG
CGAAAGACTTTGTAGCTTGGTCGACGATTGTTTTAAACAATGTGCTGAGG
ATTCGTCATTTATTTTGAAATATTACAGTGCTCGTCTCATGTTGAAGAAG
ATGATTCCAGAAGTTTATAGTTATAGCGATTATGTCAATGAAAGAGAGAA
AGACGTTTGCATTTGCCGGGATTCAGTGTATGGAAATATGATTGAATGCA
TAAATAAAGATTGTGCTACGCGTTGGTTTCATGCACATTGTGTGAAGATC
AAACCGGAATTTGCTGATATCTGGTTGTGCGAGGCCTGCCGAGAGAATTG
CTGTAGATAGAATATTTGAATCTGGAATTAGATTAAAAGAGAGATCGGAA
G
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protein sequence of SMED30024073-orf-1

>SMED30024073-orf-1 ID=SMED30024073-orf-1|Name=SMED30024073-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=179bp
MTEHFKIKIKKKLQKFTNDFNLLSHEIQLKDQLVQSLQKEYKETLKSTLA
NCSNIKNVEKIIVKIQNLIDEKVECSERLCSLVDDCFKQCAEDSSFILKY
YSARLMLKKMIPEVYSYSDYVNEREKDVCICRDSVYGNMIECINKDCATR
WFHAHCVKIKPEFADIWLCEACRENCCR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR001965Znf_PHD
IPR013083Znf_RING/FYVE/PHD
IPR019786Zinc_finger_PHD-type_CS
IPR011011Znf_FYVE_PHD
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0005515protein binding
GO:0046872metal ion binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0016569covalent chromatin modification