SMED30025741

Overview
NameSMED30025741
Smed IDSMED30025741
Length (bp)592
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 SMED30025741 (SMED30025741) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025741 (SMED30025741) 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 SMED30025741 (SMED30025741) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025741 (SMED30025741) 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




SMED30025741

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30025741h1SMcG0005543 SmedASXL_014068SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30025741h1SMcG0005543 SmedASXL_014068SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30025741h1SMcG0005543 SmedASXL_014068SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig55562newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig55562uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig11010newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig11010uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig53057newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005543 Contig53057uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005534 Contig55562newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30025741h1SMcG0005534 Contig55562uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Category 2 cellSMED30025741h1SMcG0005543 dd_Smed_v6_69_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30025741h1SMcG0005535 dd_Smed_v6_69_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025741 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010791:11787..12433 -2820
v31.012923:3724..4375 -2298
v31.027295:3880..4528 -2139
Homology
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000024991.1 (SMESG000024991.1)

HSP 1 Score: 187.193 bits (474), Expect = 1.849e-61
Identity = 93/96 (96.88%), Postives = 93/96 (96.88%), Query Frame = 3
Query:  207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR 494
            MRLDKIQKREMSAEC GELQKLRD F KATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR
Sbjct:    1 MRLDKIQKREMSAECLGELQKLRDDFAKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR 96          
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000054781.1 (SMESG000054781.1)

HSP 1 Score: 120.553 bits (301), Expect = 2.649e-35
Identity = 63/97 (64.95%), Postives = 73/97 (75.26%), Query Frame = 3
Query:  207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494
            MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQY + + K    Y  N +KC + I   ++ECR G  + +  + EE +KINNACENE R
Sbjct:    1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESR 97          
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025013.1 (SMESG000025013.1)

HSP 1 Score: 120.553 bits (301), Expect = 2.649e-35
Identity = 63/97 (64.95%), Postives = 73/97 (75.26%), Query Frame = 3
Query:  207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494
            MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQY + + K    Y  N +KC + I   ++ECR G  + +  + EE +KINNACENE R
Sbjct:    1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESR 97          
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025003.1 (SMESG000025003.1)

HSP 1 Score: 115.931 bits (289), Expect = 2.175e-33
Identity = 60/95 (63.16%), Postives = 72/95 (75.79%), Query Frame = 3
Query:  213 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494
            LDKIQKREMSAECQGELQKLRDGFDKATDELDKKC+SQY + + K    Y  N +KC + I   ++ECR G+ + +  + EE +KINNACENE R
Sbjct:    9 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCKSQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGLVKHTKWFSEEDEKINNACENESR 103          
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025000.1 (SMESG000025000.1)

HSP 1 Score: 77.411 bits (189), Expect = 2.870e-18
Identity = 43/118 (36.44%), Postives = 71/118 (60.17%), Query Frame = 3
Query:  141 MAKLIFIVLAVLFVYGECRRFKMRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKC-INEIPMTQECRKGITQISIRYGEEIQKINNACENEY 491
            M K++ +   + FV  ECR F++RLDKI KREMS+EC+ EL+KL D F  A +++D  C++ Y +   K    Y    +KC ++   MT++C+  + ++   + E   K++  C+NEY
Sbjct:    1 MNKILLLTFVIFFVSVECR-FRLRLDKIAKREMSSECKAELKKLDDQFTAAANKIDDDCDAVYVKWSKKYLPEYVALKEKCGLDTSKMTKDCKTELKRLFNLFAEGNYKVDLECDNEY 117          
The following BLAST results are available for this feature:
BLAST of SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 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 SMED30025741 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024991.11.849e-6196.88SMESG000024991.1[more]
SMESG000054781.12.649e-3564.95SMESG000054781.1[more]
SMESG000025013.12.649e-3564.95SMESG000025013.1[more]
SMESG000025003.12.175e-3363.16SMESG000025003.1[more]
SMESG000025000.12.870e-1836.44SMESG000025000.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025741 ID=SMED30025741|Name=SMED30025741|organism=Schmidtea mediterranea sexual|type=transcript|length=592bp
AATAAAATCATTGATAAGCTTTCTGGAACTAGAACGGGTGACATTGGGTT
TGCTCATCAACCGTAACTCGCATGTCTCTTCTGTTCGTCAGCTCCAACTA
TAAATATTTGAGAAAAATGTTTTTCTTTAACTATTTCATAATGGCAAAAT
TAATTTTTATTGTTCTCGCTGTGTTATTTGTTTACGGAGAATGCCGCCGA
TTTAAAATGCGACTCGACAAAATACAGAAACGAGAAATGAGTGCCGAATG
TCAAGGAGAACTGCAAAAGTTGCGCGATGGTTTCGACAAAGCTACGGACG
AGCTCGATAAAAAATGTGAAAGTCAATATGGGCAAGAAAAAGCAAAGGAG
GCAAAATTTTATCAAGATAATTTTAAAAAATGTATTAATGAAATACCGAT
GACGCAAGAATGCCGCAAGGGCATTACTCAAATTAGTATTAGGTACGGCG
AAGAAATCCAAAAAATAAACAATGCATGCGAAAATGAATATCGAAAACTT
TTAGAGGAATTAAATGCAAATGAAGATAATCTGAAAAAGAAATGTGCATA
AATTCAATAAAATTATTTTGTTAATATATCATTATTTTTCGA
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protein sequence of SMED30025741-orf-1

>SMED30025741-orf-1 ID=SMED30025741-orf-1|Name=SMED30025741-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp
MSLLFVSSNYKYLRKMFFFNYFIMAKLIFIVLAVLFVYGECRRFKMRLDK
IQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDN
FKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYRKLLEELNAN
EDNLKKKCA*
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Aliases
The feature 'SMED30025741' has the following synonyms
Synonym
prog-2-1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0002032epidermal cell
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 126..159
NoneNo IPR availableCOILSCoilCoilcoord: 64..84
NoneNo IPR availableTMHMMTMhelixcoord: 17..39