SMED30013016

Overview
NameSMED30013016
Smed IDSMED30013016
Length (bp)1022
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30013016 (SMED30013016) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013016 (SMED30013016) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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



SMED30013016

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30013016h1SMcG0006797 SmedASXL_078558SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30013016h1SMcG0006797 SmedASXL_078558SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30013016h1SMcG0006797 SmedASXL_073752SmedAsxl_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 SMED30013016 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1)

HSP 1 Score: 97.0561 bits (240), Expect = 9.238e-32
Identity = 47/70 (67.14%), Postives = 54/70 (77.14%), Query Frame = -2 
Query:  218 EIELSFVAIKREPGSIPAQVIRGQAEFLLARL*EHQRQTNAQVERANRYLAKVNEDIADGEFPVRTGMLP 427
            EI+L FVAIKREPG  PA+ IRGQAEFLLARL EHQRQTN QV+RA R+LA++N+ IA G  P   G  P
Sbjct:   55 EIDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAIATGAIPSTDGYAP 124

HSP 2 Score: 40.0466 bits (92), Expect = 9.238e-32
Identity = 16/26 (61.54%), Postives = 20/26 (76.92%), Query Frame = -1 
Query:  168 IPSTDGYAPP*NTSFNLDDSKLDARS 245
            IPSTDGYAPP N S++L++  LD  S
Sbjct:  116 IPSTDGYAPPYNVSYDLNNPNLDEES 141

HSP 3 Score: 39.2762 bits (90), Expect = 9.238e-32
Identity = 15/30 (50.00%), Postives = 21/30 (70.00%), Query Frame = -3 
Query:  436 ANQTNRCRQAMWDAGFTVSQVKESRFNAQQ 525
            A    RC+Q++WDAGF+VS V+E R   Q+
Sbjct:   22 ARSATRCQQSLWDAGFSVSPVREFRAGIQR 51
[Close]
BLAST of SMED30013016 vs. Planmine SMEST
Match: SMESG000025513.1 (SMESG000025513.1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.020e-31
Identity = 55/81 (67.90%), Postives = 58/81 (71.60%), Query Frame = -2 
Query:  188 EEIELSFVAIKREPGSIPAQVIRGQAEFLLARL*EHQRQTNAQVERANRYLAKVNEDIADGEFPVRTGMLPRKTPRLTSMT 430
            EEIEL FVAIKREPG  PA+ I  QAEFLLARL EHQRQTNAQVE+A RYL         G+FPVRT  L R TP L SMT
Sbjct:   65 EEIELQFVAIKREPGHNPAREIWCQAEFLLARLEEHQRQTNAQVEKARRYL---------GKFPVRTDTLLRTTPLLNSMT 136

HSP 2 Score: 56.225 bits (134), Expect = 1.020e-31
Identity = 25/30 (83.33%), Postives = 26/30 (86.67%), Query Frame = -3 
Query:  436 ANQTNRCRQAMWDAGFTVSQVKESRFNAQQ 525
            A+  NRCRQ MWDAGFTVSQVKESRFN QQ
Sbjct:   33 AHVANRCRQVMWDAGFTVSQVKESRFNTQQ 62
[Close]
BLAST of SMED30013016 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1)

HSP 1 Score: 96.6709 bits (239), Expect = 1.161e-31
Identity = 47/70 (67.14%), Postives = 54/70 (77.14%), Query Frame = -2 
Query:  218 EIELSFVAIKREPGSIPAQVIRGQAEFLLARL*EHQRQTNAQVERANRYLAKVNEDIADGEFPVRTGMLP 427
            EI+L FVAIKREPG  PA+ IRGQAEFLLARL EHQRQTN QV+RA R+LA++N+ IA G  P   G  P
Sbjct:   55 EIDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAIATGAIPSTDGYAP 124

HSP 2 Score: 40.0466 bits (92), Expect = 1.161e-31
Identity = 16/26 (61.54%), Postives = 20/26 (76.92%), Query Frame = -1 
Query:  168 IPSTDGYAPP*NTSFNLDDSKLDARS 245
            IPSTDGYAPP N S++L++  LD  S
Sbjct:  116 IPSTDGYAPPYNVSYDLNNPNLDEES 141

HSP 3 Score: 39.2762 bits (90), Expect = 1.161e-31
Identity = 15/30 (50.00%), Postives = 21/30 (70.00%), Query Frame = -3 
Query:  436 ANQTNRCRQAMWDAGFTVSQVKESRFNAQQ 525
            A    RC+Q++WDAGF+VS V+E R   Q+
Sbjct:   22 ARSATRCQQSLWDAGFSVSPVREFRAGIQR 51
[Close]
BLAST of SMED30013016 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1)

HSP 1 Score: 88.1965 bits (217), Expect = 1.323e-29
Identity = 43/64 (67.19%), Postives = 52/64 (81.25%), Query Frame = -2 
Query:  239 EEIELSFVAIKREPGSIPAQVIRGQAEFLLARL*EHQRQTNAQVERANRYLAKVNEDIADGEFP 430
            E+++L FVAIKREPG  PA+ IRGQAEFLLARL EHQRQT  QV RA R+LA++N+ IA G+ P
Sbjct:  406 EKVDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAIATGDIP 469

HSP 2 Score: 41.2022 bits (95), Expect = 1.323e-29
Identity = 19/34 (55.88%), Postives = 22/34 (64.71%), Query Frame = -1 
Query:  144 IPSTDGYAPP*NTSFNLDDSKLDARSTAITSIGP 245
            IPSTD YAPP N SFNLDD  L   + A+  + P
Sbjct:  468 IPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVP 501

HSP 3 Score: 39.6614 bits (91), Expect = 1.323e-29
Identity = 16/25 (64.00%), Postives = 19/25 (76.00%), Query Frame = -3 
Query:  451 ANQTNRCRQAMWDAGFTVSQVKESR 525
            A    RCRQ +WDAGF+VS V+ESR
Sbjct:  374 ARSVARCRQVLWDAGFSVSPVRESR 398
[Close]
BLAST of SMED30013016 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1)

HSP 1 Score: 95.1301 bits (235), Expect = 7.052e-29
Identity = 48/73 (65.75%), Postives = 52/73 (71.23%), Query Frame = -2 
Query:  218 EFEEIELSFVAIKREPGSIPAQVIRGQAEFLLARL*EHQRQTNAQVERANRYLAKVNEDIADGEFPVRTGMLP 436
            + EE+EL FVAIKREPG  PA+ IRGQAEFLLARL EHQRQT+ QV RA  YLA VNED A G      G  P
Sbjct: 1154 QMEEVELPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTDLQVARARLYLANVNEDKAAGRIACTEGYAP 1226

HSP 2 Score: 51.2174 bits (121), Expect = 7.052e-29
Identity = 21/30 (70.00%), Postives = 24/30 (80.00%), Query Frame = -3 
Query:  436 ANQTNRCRQAMWDAGFTVSQVKESRFNAQQ 525
            A+  NRCRQAMWDAGFT+SQV+ESR    Q
Sbjct: 1124 AHAANRCRQAMWDAGFTISQVRESRSGTLQ 1153
The following BLAST results are available for this feature:
BLAST of SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 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 SMED30013016 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000003962.19.238e-3267.14SMESG000003962.1[more]
SMESG000025513.11.020e-3167.90SMESG000025513.1[more]
SMESG000003962.11.161e-3167.14SMESG000003962.1[more]
SMESG000023390.11.323e-2967.19SMESG000023390.1[more]
SMESG000019398.17.052e-2965.75SMESG000019398.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013016 ID=SMED30013016|Name=SMED30013016|organism=Schmidtea mediterranea sexual|type=transcript|length=1022bp
CAACACTCTGGTTAAAGTGCTTCATCTACTCACCAGTAGCTCCGCAAACA
TTCGAAGAGTATTCTTCTCGAGCGTAAGGGTGCTCGTGGTGGCCATCGGG
TCGTCTTTCTTCCATCCTCATTTCACGGGGAAGAATCCTCCGTGGGACCA
ATCGATGTGATTGCCGTAGACCTCGCATCTAGCTTACTGTCATCGAGGTT
AAACGAGGTGTTTTACGGGGGAGCATACCCGTCCGTACTGGGAATTCTCC
ATCCGCAATATCTTCGTTAACTTTAGCCAGATAACGATTGGCTCTCTCCA
CTTGTGCATTGGTTTGACGCTGATGCTCTTAGAGGCGAGCTAGGAGAAAT
TCAGCTTGTCCCCGGATCACCTGTGCCGGGATGCTTCCTGGTTCCCGCTT
TATAGCGACGAACGAAAGTTCGATCTCCTCGAATTCTGTTGCGCGTTGAA
TCTCGATTCCTTCACCTGGGAGACGGTGAATCCCGCGTCCCACATAGCTT
GGCGACATCGGTTAGTCTGATTAGCTATGGGTTGCCTAAAAGATTGTACC
ATATATCGTCAAGTCGATCTCATGGTGTTTTTGGCTTGTTCGTATTGAAC
TCATCTCATTTTCGTGGTCAATAAGAACTGTGGATGCGAAGTAATTTATT
CCTAGGTCGGCCGATGTTTGAATGTTTGATACTATAGGTGATCTGATTAG
TGTAACCTTGACCCCAACTATAATTACTCTCGATCCAACGGTTACCCCTT
GCCACGCAACGTTGGTAATCCAACCACTGGTCATAGGATCGCCAAAGGTG
AGCGCCACGAAGGAACTACTTAGTACCGATACCATAGCGGGTTCAACGCA
CTACCGATAGAAGGTACGCGATAAAACTTTAGCGGCTGAGATGATCGGTT
TACGTAGAAATAGTCTATCCAAAAAAAGTCGGGTTGCTCTCATCGTGCCA
GTTAGTTGATCAGCACATTTATACTTGAACGTCAAGTTCGTATCAATTTT
CTGCATAGATGACTTAAATTCG
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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