SMED30015373

Overview
NameSMED30015373
Smed IDSMED30015373
Length (bp)2099
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 SMED30015373 (SMED30015373) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015373 (SMED30015373) 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 SMED30015373 (SMED30015373) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015373 (SMED30015373) 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



SMED30015373

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30015373SMESG000000625.1 dd_Smed_v4_1629_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015373SMESG000000625.1 dd_Smed_v4_1629_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30015373SMESG000000625.1 dd_Smed_v4_1629_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30015373SMESG000000625.1 dd_Smed_v4_1629_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015373SMESG000000625.1 Contig46185newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30015373SMESG000000625.1 Contig46185uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 2 cellSMED30015373SMESG000000625.1 dd_Smed_v6_1629_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30015373SMESG000000625.1 dd_Smed_v6_1629_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015373SMESG000000625.1 dd_Smed_v4_1629_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
SMED30015373 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001262:72712..90959 +9027
Homology
[Close]
BLAST of SMED30015373 vs. Planmine SMEST
Match: SMESG000000625.1 (SMESG000000625.1)

HSP 1 Score: 822.772 bits (2124), Expect = 0.000e+0
Identity = 597/601 (99.33%), Postives = 598/601 (99.50%), Query Frame = 1 
Query:   91 MTTITGHYNVTVNSRYYVFLQEDLESAEPHVLMANVEKKRELXXXXXXXXXXXXXXXQVAEAIKESVKVENKIDEIIKXXXXXXXXXXXXXXXXXXXXXXXFVDEIPMEXXXXXXXXXXXXXXXXXXXXXXXXXXXXEDKTYNYDDSSHQKSQDSEHNKFASNSRGGRPFRKERSEGESSGRFGYFEEXXXXXXXXXXXXXXXXXXXXXXXXXXXADRLNSDRQPFERSNYERNGNERFNNDRDGNERNGFDRNRTYNDENMKIDIIPENMGTFEDMXXXXXXXXXXXXXXXXXXXFNRYNASTNENDFENNKIGYFDENVENREFXXXXXXXXXXXXXXXXXDSWRQRGSDRDENHDEGPSNNMKTETHDVPTVEKWPECDEDLDPESNNIEPIVNSTGVTESDFNDFKKSNWGEIEDDPVELKPTNEHMTLEEYRALHGKERVFIQEGKETRKANDGQDVFSGMEEYRKGRLVEEQGDDHDSHENQHGRQKQSIPLAIRFSRNTEYGDSNNFEQQTVENRNFSRGYYKNENKXXXXXXXXXXXXXXXXXXXFNTYXXXXXXXXXXXXXXXXPYPPKRKEDQVDGVNINLGNEDEFPTLS 1893
            MTTITGHYNVTVNSRYYVFLQEDLESAEPHVLMANVEKKRELRKESKTKAKKEKRSKQVAEAIKESVKVENKIDEIIKPEMEIVVEHEPEVIECP+EIREPFVDEIPMENKNDRGSRGRGNNRRQNGGPRRGGYPRNEDKTYNYDDSSHQKSQDSEHNKFASNSRGGRPFRKER EGESSGRFGYFEENSSTNTRGNSVRRRSSGRPSGRYNRGGADRLNSDRQPFERSNYERNGNERFNNDRDGNERNGFDRNRT NDENMKIDIIPENMGTFEDMSSRPPRSSRGRYPRSYRGGFNRYNASTNENDFENNKIGYFDENVENREFRGSRGRSRGRGMRRGRGDSWRQRGSDRDENHDE PSNNMKTETHDVPTVEKWPECDEDLDPESNNIEPIVNSTGVTESDFNDFKKSNWGEIEDDPVELKPTNEHMTLEEYRALHGKERVFIQEGKETRKANDGQDVFSGMEEYRKGRLVEEQGDDHDSHENQHGRQKQSIPLAIRFSRNTEYGDSNNFEQQTVENRNFSRGYYKNENKSRGDNSSSGDRGRSRGGSDFNTYGRGRDFNRGRGRFNRNPYPPKRKEDQVDGVNINLGNEDEFPTLS
Sbjct:    1 MTTITGHYNVTVNSRYYVFLQEDLESAEPHVLMANVEKKRELRKESKTKAKKEKRSKQVAEAIKESVKVENKIDEIIKPEMEIVVEHEPEVIECPVEIREPFVDEIPMENKNDRGSRGRGNNRRQNGGPRRGGYPRNEDKTYNYDDSSHQKSQDSEHNKFASNSRGGRPFRKERPEGESSGRFGYFEENSSTNTRGNSVRRRSSGRPSGRYNRGGADRLNSDRQPFERSNYERNGNERFNNDRDGNERNGFDRNRTDNDENMKIDIIPENMGTFEDMSSRPPRSSRGRYPRSYRGGFNRYNASTNENDFENNKIGYFDENVENREFRGSRGRSRGRGMRRGRGDSWRQRGSDRDENHDEDPSNNMKTETHDVPTVEKWPECDEDLDPESNNIEPIVNSTGVTESDFNDFKKSNWGEIEDDPVELKPTNEHMTLEEYRALHGKERVFIQEGKETRKANDGQDVFSGMEEYRKGRLVEEQGDDHDSHENQHGRQKQSIPLAIRFSRNTEYGDSNNFEQQTVENRNFSRGYYKNENKSRGDNSSSGDRGRSRGGSDFNTYGRGRDFNRGRGRFNRNPYPPKRKEDQVDGVNINLGNEDEFPTLS 601
The following BLAST results are available for this feature:
BLAST of SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 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 SMED30015373 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000000625.10.000e+099.33SMESG000000625.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015373 ID=SMED30015373|Name=SMED30015373|organism=Schmidtea mediterranea sexual|type=transcript|length=2099bp
GTGAGCGGTGTTTAAATAATTCATTTAAAATAAAAAGGTTTCAGTTATAT
AGACGATGCAATTTCATTAAAACTATCCAAAAATATCGATATGACAACTA
TTACCGGACATTATAACGTTACAGTCAATTCTAGATACTATGTTTTTCTC
CAAGAGGACTTGGAATCTGCTGAACCTCATGTTTTGATGGCGAATGTTGA
AAAAAAACGAGAACTTCGCAAAGAAAGCAAAACTAAAGCAAAAAAAGAAA
AACGTAGTAAACAAGTAGCAGAAGCAATTAAAGAAAGTGTCAAAGTAGAA
AATAAGATTGATGAAATAATTAAACCTGAAATGGAAATTGTAGTTGAACA
CGAACCCGAAGTTATAGAGTGCCCTATTGAAATCCGAGAACCTTTTGTTG
ACGAAATACCTATGGAAAACAAAAACGATCGTGGTAGTAGAGGACGTGGT
AATAACAGACGTCAGAATGGTGGACCAAGACGAGGAGGGTATCCGAGAAA
TGAAGATAAAACTTACAATTATGATGATAGTAGTCATCAGAAATCTCAAG
ATAGCGAACATAATAAATTTGCATCTAATAGTAGGGGTGGTAGACCATTT
AGAAAAGAGAGATCAGAAGGTGAAAGTTCTGGCAGATTCGGTTATTTCGA
AGAAAATTCAAGTACTAACACCCGCGGAAATTCAGTAAGGCGAAGATCAT
CTGGTAGACCAAGTGGACGATACAATCGCGGAGGTGCTGATAGATTAAAT
AGTGACAGACAACCATTTGAGCGATCGAATTATGAAAGAAACGGAAATGA
AAGATTTAATAACGATCGCGATGGAAATGAAAGAAATGGATTTGATAGAA
ATAGAACTTATAATGACGAAAATATGAAAATTGATATTATACCAGAAAAC
ATGGGAACATTTGAAGATATGTCATCCAGGCCGCCAAGAAGTAGCCGGGG
GCGGTATCCTAGATCTTATCGAGGAGGATTCAATCGATATAATGCTTCAA
CTAATGAAAATGATTTTGAAAACAACAAAATCGGCTATTTTGATGAAAAT
GTGGAAAACAGGGAGTTTAGAGGTAGTCGTGGTAGGTCTAGAGGCAGAGG
TATGAGAAGAGGTCGTGGTGATTCTTGGAGACAAAGAGGAAGTGATCGTG
ATGAAAATCATGACGAAGGTCCTTCCAATAATATGAAAACTGAAACCCAC
GATGTGCCTACTGTTGAGAAATGGCCAGAATGTGATGAGGACCTCGATCC
TGAATCAAATAATATCGAACCGATCGTTAATTCTACTGGTGTAACCGAAT
CAGATTTTAACGACTTTAAAAAGTCTAATTGGGGAGAAATAGAGGATGAT
CCGGTTGAATTGAAACCGACTAACGAGCACATGACTCTAGAAGAATATCG
AGCACTCCACGGTAAAGAAAGGGTATTTATTCAAGAGGGAAAAGAAACAC
GGAAAGCAAATGATGGTCAGGATGTTTTCAGTGGAATGGAAGAGTATCGA
AAAGGTCGATTGGTTGAAGAACAAGGTGACGATCACGATAGTCATGAAAA
TCAGCATGGCCGGCAAAAACAATCTATTCCATTAGCTATTCGATTCAGTC
GGAACACTGAATACGGTGACTCAAACAATTTCGAACAGCAAACTGTTGAA
AATAGAAACTTTTCCAGAGGATATTATAAAAACGAAAATAAATCTCGTGG
TGATAATTCATCCTCGGGAGACCGTGGGAGGTCTCGAGGAGGTTCTGATT
TTAATACTTATGGCAGAGGTCGGGATTTCAACAGAGGAAGAGGGCGATTC
AATAGAAATCCTTATCCCCCAAAAAGAAAAGAAGATCAAGTTGACGGAGT
CAACATCAATCTAGGAAACGAAGATGAATTCCCAACATTGAGCTAATATC
AAAAAGCTGTAACAGTGAATAATAATTTCTGTATGTGTGTGTGTACTAAG
AATTGCGAAATATTTAAAATTTCGTATCGTATAATTTTAGCAGTAATATT
ATCCCATATTCATACTTTTATCGTAGTTTGTTAAATTAAAAGCAATTTTA
ATGTTTTTGTGTTTAATCATAAATAAAGTACATTAATTTTAAAAAAAAA
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protein sequence of SMED30015373-orf-1

>SMED30015373-orf-1 ID=SMED30015373-orf-1|Name=SMED30015373-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=602bp
MTTITGHYNVTVNSRYYVFLQEDLESAEPHVLMANVEKKRELRKESKTKA
KKEKRSKQVAEAIKESVKVENKIDEIIKPEMEIVVEHEPEVIECPIEIRE
PFVDEIPMENKNDRGSRGRGNNRRQNGGPRRGGYPRNEDKTYNYDDSSHQ
KSQDSEHNKFASNSRGGRPFRKERSEGESSGRFGYFEENSSTNTRGNSVR
RRSSGRPSGRYNRGGADRLNSDRQPFERSNYERNGNERFNNDRDGNERNG
FDRNRTYNDENMKIDIIPENMGTFEDMSSRPPRSSRGRYPRSYRGGFNRY
NASTNENDFENNKIGYFDENVENREFRGSRGRSRGRGMRRGRGDSWRQRG
SDRDENHDEGPSNNMKTETHDVPTVEKWPECDEDLDPESNNIEPIVNSTG
VTESDFNDFKKSNWGEIEDDPVELKPTNEHMTLEEYRALHGKERVFIQEG
KETRKANDGQDVFSGMEEYRKGRLVEEQGDDHDSHENQHGRQKQSIPLAI
RFSRNTEYGDSNNFEQQTVENRNFSRGYYKNENKSRGDNSSSGDRGRSRG
GSDFNTYGRGRDFNRGRGRFNRNPYPPKRKEDQVDGVNINLGNEDEFPTL
S*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000034epidermis
PLANA:0000429neoblast
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 35..55
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 103..120
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 527..543
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 477..601
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 166..181
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 560..585
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 326..380
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 184..205
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 216..264
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 40..59
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 326..404
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 491..526
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 133..158
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 103..292