SMED30005189

Overview
NameSMED30005189
Smed IDSMED30005189
Length (bp)1534
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 SMED30005189 (SMED30005189) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005189 (SMED30005189) 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 SMED30005189 (SMED30005189) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005189 (SMED30005189) 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



SMED30005189

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 cellSMED30005189SMESG000023929.1 SmedASXL_007153SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30005189SMESG000023929.1 SmedASXL_007153SmedAsxl_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
SMED30005189 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002660:31610..37720 +7471
v31.008918:24789..31309 -7385
Homology
[Close]
BLAST of SMED30005189 vs. Planmine SMEST
Match: SMESG000023929.1 (SMESG000023929.1)

HSP 1 Score: 880.167 bits (2273), Expect = 0.000e+0
Identity = 431/435 (99.08%), Postives = 432/435 (99.31%), Query Frame = 2 
Query:   41 MKIFICLFSSSISNVKSFNIEVSDNYLIDSLSSLINSEQNISNCEYEFVYKKLFCQSGKTLHELDIVENSKIYAIKKNLKTLKRPSNDNLHSLLNCGSSTKELCTISNKNYFEHISWKNGGLNEIQAQMTEMITENPSLIESFILQPDVENLVNNPLNISTLYSANPIIKDTMNNHPDKVKFFTDASQYIWIKNIMDDPKKYDNVMENYSENLKQAINSKRYRRMTELFNSTVDKTAAKRESAADEEEILQNNLETYCGNLMEPILKSPYANHIIDIIGTDNHLSDSILKCCPYGSNLDETSLAAIQNVMPSVIGRWKQAMVHSNDPEKVLEYFQNNPIELDGDEAQILEQVTEKCEHKEIDISAIDEPIISQLVQKITNRFEGGK-VADKGDCKSFDRELEALNEMGFTDNIVNLEAVTKEHGNLDRAIYRLLA 1342
            MKIFICLFSSSISNVKSFNIEVSDNYLIDSLSSLINSEQNISNCEYEFVYKKLFCQSGKTLHELDIVENSKIYAIKKNLKTLKRPSNDNLHSLLNCGSSTK+LCTISNKNYFEHISWKNGGLNEIQAQMTEMITENPSLIESFILQPDVENLVNNPLNISTLYSANPIIKDTMNNHPDKVKFFTD SQYIWIKNIMDDPKKYDNVMENYSENLKQAINSKRYRRMTELFNSTVDKTAAKRESAADEEEILQNNLETYCGNLMEPILKSPYANHIIDIIGTDNHLSDSILKCCPYGSNLDETSLAAIQNVMPSVIGRWKQAMVHSNDPEKVLEYFQNNPIELDGDEAQILEQVTEKCEHKEIDISAIDEPIISQLVQKITNRFEGGK  ADKGDCKSFDRELEALNEMGFTDNIVNLEAVTKEHGNLDRAIYRLLA
Sbjct:    1 MKIFICLFSSSISNVKSFNIEVSDNYLIDSLSSLINSEQNISNCEYEFVYKKLFCQSGKTLHELDIVENSKIYAIKKNLKTLKRPSNDNLHSLLNCGSSTKKLCTISNKNYFEHISWKNGGLNEIQAQMTEMITENPSLIESFILQPDVENLVNNPLNISTLYSANPIIKDTMNNHPDKVKFFTDTSQYIWIKNIMDDPKKYDNVMENYSENLKQAINSKRYRRMTELFNSTVDKTAAKRESAADEEEILQNNLETYCGNLMEPILKSPYANHIIDIIGTDNHLSDSILKCCPYGSNLDETSLAAIQNVMPSVIGRWKQAMVHSNDPEKVLEYFQNNPIELDGDEAQILEQVTEKCEHKEIDISAIDEPIISQLVQKITNRFEGGKEGADKGDCKSFDRELEALNEMGFTDNIVNLEAVTKEHGNLDRAIYRLLA 435
The following BLAST results are available for this feature:
BLAST of SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 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 SMED30005189 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000023929.10.000e+099.08SMESG000023929.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005189 ID=SMED30005189|Name=SMED30005189|organism=Schmidtea mediterranea sexual|type=transcript|length=1534bp
TTAAATTCATACTAGACTTATTTTTTTCAAAAGATATAAAATGAAAATTT
TTATTTGCCTATTTAGTTCTTCTATTTCTAATGTTAAAAGTTTTAATATT
GAAGTCAGTGACAACTATTTAATAGATTCGTTATCATCGTTAATTAACTC
TGAACAAAACATTTCTAACTGTGAATATGAATTCGTATATAAGAAGCTTT
TTTGTCAATCTGGTAAAACATTACATGAATTAGATATAGTAGAAAACAGC
AAAATTTATGCTATTAAAAAAAATTTGAAAACATTAAAACGTCCATCGAA
TGATAATTTACATTCATTACTTAATTGCGGTTCATCTACTAAGGAACTAT
GTACCATATCAAATAAGAATTATTTTGAACATATTTCATGGAAAAATGGT
GGCTTAAATGAAATTCAAGCTCAAATGACTGAAATGATCACAGAAAATCC
AAGTTTAATTGAGTCATTTATTCTACAACCAGATGTAGAAAATCTAGTTA
ATAATCCATTAAATATTTCTACTCTTTATTCAGCTAACCCTATCATAAAG
GATACAATGAATAATCATCCCGATAAAGTAAAATTTTTCACTGATGCGTC
ACAGTACATTTGGATAAAGAACATAATGGATGATCCGAAAAAATACGATA
ATGTCATGGAAAATTACTCTGAAAATCTCAAACAAGCTATAAATTCTAAA
CGATATCGACGAATGACAGAGTTATTCAACAGTACTGTTGATAAAACAGC
CGCTAAGCGGGAATCAGCAGCAGATGAAGAAGAGATATTGCAGAATAATC
TGGAAACGTATTGCGGAAATTTAATGGAGCCAATCTTGAAATCCCCATAT
GCCAATCACATTATCGACATTATTGGCACAGACAATCATTTATCTGATTC
AATTCTCAAATGTTGTCCATATGGATCGAATTTGGATGAAACTAGTTTGG
CGGCAATCCAAAATGTGATGCCTTCTGTTATTGGTCGATGGAAACAAGCG
ATGGTGCATTCAAATGATCCTGAGAAAGTGTTAGAATACTTTCAAAATAA
TCCAATCGAATTGGACGGGGACGAAGCCCAAATATTGGAACAAGTTACTG
AGAAATGCGAACATAAAGAAATAGACATATCTGCCATTGATGAGCCAATC
ATTTCACAGCTTGTGCAAAAAATCACCAATCGATTCGAGGGTGGAAAGGT
AGCCGATAAAGGTGATTGTAAGTCATTCGATAGAGAATTAGAGGCGTTAA
ATGAAATGGGGTTCACCGATAATATTGTAAATCTAGAAGCTGTTACCAAG
GAACATGGGAACTTAGATAGAGCCATCTATCGGTTATTGGCATAGATCTT
ATTCTCGAGTGTAATCTCTCCATTGTTCTGGTTTCGTATTAATAGAATCA
ACTGTGTCCTACTTATTGAGTTTTTTTTATTACAATTGTATTCTATATTA
CAGTAATTAAACAAATCAAGTTCATAAATGATGCCATGTGACTAGGGGAG
AAGAAAGTGTATTAGAAATATGATGTCATAATAT
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protein sequence of SMED30005189-orf-1

>SMED30005189-orf-1 ID=SMED30005189-orf-1|Name=SMED30005189-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=435bp
MKIFICLFSSSISNVKSFNIEVSDNYLIDSLSSLINSEQNISNCEYEFVY
KKLFCQSGKTLHELDIVENSKIYAIKKNLKTLKRPSNDNLHSLLNCGSST
KELCTISNKNYFEHISWKNGGLNEIQAQMTEMITENPSLIESFILQPDVE
NLVNNPLNISTLYSANPIIKDTMNNHPDKVKFFTDASQYIWIKNIMDDPK
KYDNVMENYSENLKQAINSKRYRRMTELFNSTVDKTAAKRESAADEEEIL
QNNLETYCGNLMEPILKSPYANHIIDIIGTDNHLSDSILKCCPYGSNLDE
TSLAAIQNVMPSVIGRWKQAMVHSNDPEKVLEYFQNNPIELDGDEAQILE
QVTEKCEHKEIDISAIDEPIISQLVQKITNRFEGGKVADKGDCKSFDREL
EALNEMGFTDNIVNLEAVTKEHGNLDRAIYRLLA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002056medial muscle cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR015496Ubiquilin
IPR029071Ubiquitin-like_domsf
IPR009060UBA-like_sf
IPR015940UBA
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR015940Ubiquitin-associated domainSMARTSM00165uba_6coord: 397..435
e-value: 1.2E-4
score: 31.5
IPR015940Ubiquitin-associated domainPROSITEPS50030UBAcoord: 396..435
score: 9.8
NoneNo IPR availableGENE3DG3DSA:1.10.8.10coord: 391..435
e-value: 2.2E-9
score: 38.9
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 1..83
e-value: 4.0E-5
score: 25.0
NoneNo IPR availableCDDcd17039Ubl_ubiquitin_likecoord: 16..73
e-value: 3.64345E-4
score: 36.8054
IPR015496UbiquilinPANTHERPTHR10677UBIQUILINcoord: 17..434
IPR009060UBA-like superfamilySUPERFAMILYSSF46934UBA-likecoord: 396..434
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 13..78