SMED30022396

Overview
NameSMED30022396
Smed IDSMED30022396
Length (bp)442
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 SMED30022396 (SMED30022396) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022396 (SMED30022396) 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 SMED30022396 (SMED30022396) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022396 (SMED30022396) 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



SMED30022396

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 cellSMED30022396 SmedASXL_017146SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30022396 SmedASXL_017146SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30022396 vs. Planmine SMEST
Match: SMESG000007017.1 (SMESG000007017.1)

HSP 1 Score: 89.7373 bits (221), Expect = 1.039e-26
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:  281 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 381

HSP 2 Score: 89.7373 bits (221), Expect = 1.039e-26
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:  611 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 711

HSP 3 Score: 89.7373 bits (221), Expect = 1.039e-26
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:  941 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 1041

HSP 4 Score: 89.7373 bits (221), Expect = 1.039e-26
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct: 1271 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 1371

HSP 5 Score: 46.9802 bits (110), Expect = 1.039e-26
Identity = 25/37 (67.57%), Postives = 30/37 (81.08%), Query Frame = 1 
Query:  331 EKFICEQLM*LEEKSDKCLDKSDEENNKILEAIKCLF 441
            +K ICEQL    +KS+K LD SDE++NKILEAIKCLF
Sbjct:  391 DKSICEQLKAFGKKSEKRLDNSDEDSNKILEAIKCLF 427

HSP 6 Score: 46.9802 bits (110), Expect = 1.039e-26
Identity = 25/37 (67.57%), Postives = 30/37 (81.08%), Query Frame = 1 
Query:  331 EKFICEQLM*LEEKSDKCLDKSDEENNKILEAIKCLF 441
            +K ICEQL    +KS+K LD SDE++NKILEAIKCLF
Sbjct:  721 DKSICEQLKAFGKKSEKRLDNSDEDSNKILEAIKCLF 757

HSP 7 Score: 46.9802 bits (110), Expect = 1.039e-26
Identity = 25/37 (67.57%), Postives = 30/37 (81.08%), Query Frame = 1 
Query:  331 EKFICEQLM*LEEKSDKCLDKSDEENNKILEAIKCLF 441
            +K ICEQL    +KS+K LD SDE++NKILEAIKCLF
Sbjct: 1051 DKSICEQLKAFGKKSEKRLDNSDEDSNKILEAIKCLF 1087

HSP 8 Score: 46.9802 bits (110), Expect = 1.039e-26
Identity = 25/37 (67.57%), Postives = 30/37 (81.08%), Query Frame = 1 
Query:  331 EKFICEQLM*LEEKSDKCLDKSDEENNKILEAIKCLF 441
            +K ICEQL    +KS+K LD SDE++NKILEAIKCLF
Sbjct: 1381 DKSICEQLKAFGKKSEKRLDNSDEDSNKILEAIKCLF 1417

HSP 9 Score: 51.9878 bits (123), Expect = 1.639e-15
Identity = 32/44 (72.73%), Postives = 34/44 (77.27%), Query Frame = 2 
Query:  209 ELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:    8 ELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 51

HSP 10 Score: 46.9802 bits (110), Expect = 1.639e-15
Identity = 25/37 (67.57%), Postives = 30/37 (81.08%), Query Frame = 1 
Query:  331 EKFICEQLM*LEEKSDKCLDKSDEENNKILEAIKCLF 441
            +K ICEQL    +KS+K LD SDE++NKILEAIKCLF
Sbjct:   61 DKSICEQLKAFGKKSEKRLDNSDEDSNKILEAIKCLF 97
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BLAST of SMED30022396 vs. Planmine SMEST
Match: SMESG000007018.1 (SMESG000007018.1)

HSP 1 Score: 90.5077 bits (223), Expect = 7.998e-25
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:  260 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 360

HSP 2 Score: 40.0466 bits (92), Expect = 7.998e-25
Identity = 20/25 (80.00%), Postives = 23/25 (92.00%), Query Frame = 1 
Query:  367 EKSDKCLDKSDEENNKILEAIKCLF 441
            EKS+K LD SDE++NKILEAIKCLF
Sbjct:  369 EKSEKRLDNSDEDSNKILEAIKCLF 393

HSP 3 Score: 90.5077 bits (223), Expect = 6.524e-22
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:   52 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 152
[Close]
BLAST of SMED30022396 vs. Planmine SMEST
Match: SMESG000007018.1 (SMESG000007018.1)

HSP 1 Score: 90.5077 bits (223), Expect = 8.991e-25
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:  260 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 360

HSP 2 Score: 40.0466 bits (92), Expect = 8.991e-25
Identity = 20/25 (80.00%), Postives = 23/25 (92.00%), Query Frame = 1 
Query:  367 EKSDKCLDKSDEENNKILEAIKCLF 441
            EKS+K LD SDE++NKILEAIKCLF
Sbjct:  369 EKSEKRLDNSDEDSNKILEAIKCLF 393

HSP 3 Score: 90.5077 bits (223), Expect = 1.048e-21
Identity = 63/101 (62.38%), Postives = 68/101 (67.33%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKR--GLDNVHKSSCDVLNKDELENSKGKELGESLEII-----KSKPVVKESQFVEEIIDDLNRS 325
            A+  S L KE S     DSTV RN DI DEIVDEVS +R  GL+N  K  CD L K ELENSKGKEL ESLEI+     KSK   KE +FVEEIIDDLNRS
Sbjct:   52 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKERKVGLENGTKLICDALEKGELENSKGKELVESLEIMKSLIPKSKAGEKERRFVEEIIDDLNRS 152

HSP 4 Score: 52.7582 bits (125), Expect = 1.306e-8
Identity = 40/74 (54.05%), Postives = 43/74 (58.11%), Query Frame = 2 
Query:   59 AKGFSSLQKEVS-----DSTVTRNGDIDDEIVDEVSMKRGLDNVHKSSCDVLNKDELENSKGKELGESLEIIKS 265
            A+  S L KE S     DSTV RN DI DEIVDEVS +R                ELENSKGKEL ESLEI+KS
Sbjct:  591 AERLSKLCKEFSESILPDSTVIRNVDIVDEIVDEVSKER----------------ELENSKGKELVESLEIMKS 648
The following BLAST results are available for this feature:
BLAST of SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 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 SMED30022396 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000007017.11.039e-2662.38SMESG000007017.1[more]
SMESG000007018.17.998e-2562.38SMESG000007018.1[more]
SMESG000007018.18.991e-2562.38SMESG000007018.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022396 ID=SMED30022396|Name=SMED30022396|organism=Schmidtea mediterranea sexual|type=transcript|length=442bp
ATTAGAAACGCAGTTTAACACAATCAGTGATCTGATCTTCATTAAGAAAA
TGATATTTGCTAAAGGATTTAGTAGTTTGCAAAAAGAAGTCTCAGATTCC
ACAGTAACAAGGAATGGTGATATTGACGACGAAATTGTTGATGAAGTAAG
TATGAAACGTGGACTTGATAATGTCCACAAATCCTCGTGTGATGTTTTGA
ATAAAGATGAATTAGAGAACTCGAAAGGTAAAGAACTTGGTGAAAGTTTA
GAAATTATTAAATCAAAGCCTGTAGTGAAAGAAAGCCAATTCGTTGAAGA
AATAATTGACGATTTGAACAGATCGAAAATGAAAAATTTATCTGCGAACA
ATTAATGTGATTAGAGGAAAAGAGTGATAAGTGTTTAGATAAATCCGATG
AGGAAAATAACAAAATATTGGAAGCAATTAAATGTTTATTTG
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protein sequence of SMED30022396-orf-1

>SMED30022396-orf-1 ID=SMED30022396-orf-1|Name=SMED30022396-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
LETQFNTISDLIFIKKMIFAKGFSSLQKEVSDSTVTRNGDIDDEIVDEVS
MKRGLDNVHKSSCDVLNKDELENSKGKELGESLEIIKSKPVVKESQFVEE
IIDDLNRSKMKNLSANN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 69..95