SMED30025143

Overview
NameSMED30025143
Smed IDSMED30025143
Length (bp)1840
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 SMED30025143 (SMED30025143) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025143 (SMED30025143) 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 SMED30025143 (SMED30025143) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025143 (SMED30025143) 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



SMED30025143

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30025143SMESG000053420.1 SMESG000053412.1 SMESG000053409.1 dd_Smed_v4_3142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025143SMESG000053420.1 SMESG000053412.1 SMESG000053409.1 dd_Smed_v4_3142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30025143SMESG000053420.1 SMESG000053412.1 SMESG000053409.1 dd_Smed_v4_3142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025143SMESG000053420.1 SMESG000053412.1 SMESG000053409.1 dd_Smed_v4_3142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30025143 vs. Planmine SMEST
Match: SMESG000053420.1 (SMESG000053420.1)

HSP 1 Score: 359.762 bits (922), Expect = 3.162e-120
Identity = 171/179 (95.53%), Postives = 175/179 (97.77%), Query Frame = 1 
Query:  769 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKRVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYDHFKFLIKRENSSLLAKYEDSENRLVENVQREPQYFNCDANY 1305
            DYPILKKADNETAMIYLMNTPQHEG YPN+DQLRGCIYDVKYNGKSLNMTASSKEIGNKCK+VCLNDICNNGECFETFSDKPICDCKLTMNNGQYCN SFVQ+NDRKLHGNKEIIRME+IKLVLFNSSDKDLFHIKY HFKFLIKRENSSLLAKYEDSENR VENVQREPQYFNCDANY
Sbjct:  149 DYPILKKADNETAMIYLMNTPQHEGAYPNSDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKKVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNASFVQLNDRKLHGNKEIIRMEYIKLVLFNSSDKDLFHIKYRHFKFLIKRENSSLLAKYEDSENRFVENVQREPQYFNCDANY 327
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BLAST of SMED30025143 vs. Planmine SMEST
Match: SMESG000053420.1 (SMESG000053420.1)

HSP 1 Score: 330.487 bits (846), Expect = 1.521e-108
Identity = 157/172 (91.28%), Postives = 162/172 (94.19%), Query Frame = 1 
Query:  769 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKRVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYDHFKFLIKRENSSLLAKYEDSENRLVENVQREPQY 1284
            DYPILKKADNETAMIYLMNTPQHEG YPN+DQLRGCIYDVKYNGKSLNMTASSKEIGNKCK+VCLNDICNNGECFETFSDKPICDCKLTMNNGQYCN SFVQ+NDRKLHGNKEIIRME+IKLVLFNSSDKDLFHIKY HFKFLIKRENSSLLAKYEDSENR VE    +  Y
Sbjct:  149 DYPILKKADNETAMIYLMNTPQHEGAYPNSDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKKVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNASFVQLNDRKLHGNKEIIRMEYIKLVLFNSSDKDLFHIKYRHFKFLIKRENSSLLAKYEDSENRFVETALSKGAY 320
[Close]
BLAST of SMED30025143 vs. Planmine SMEST
Match: SMESG000053409.1 (SMESG000053409.1)

HSP 1 Score: 287.345 bits (734), Expect = 3.223e-94
Identity = 137/142 (96.48%), Postives = 140/142 (98.59%), Query Frame = 1 
Query:  769 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKRVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYDHFKF 1194
            DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCK+VCLN+ICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKY+ F F
Sbjct:   35 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKKVCLNNICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYESFFF 176
[Close]
BLAST of SMED30025143 vs. Planmine SMEST
Match: SMESG000053409.1 (SMESG000053409.1)

HSP 1 Score: 289.656 bits (740), Expect = 5.273e-94
Identity = 137/142 (96.48%), Postives = 140/142 (98.59%), Query Frame = 1 
Query:  769 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKRVCLNDICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYDHFKF 1194
            DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCK+VCLN+ICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKY+ F F
Sbjct:  106 DYPILKKADNETAMIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKKVCLNNICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKEIIRMEHIKLVLFNSSDKDLFHIKYESFFF 247
[Close]
BLAST of SMED30025143 vs. Planmine SMEST
Match: SMESG000053412.1 (SMESG000053412.1)

HSP 1 Score: 252.292 bits (643), Expect = 4.231e-81
Identity = 148/149 (99.33%), Postives = 148/149 (99.33%), Query Frame = 2 
Query: 1262 MFNGNLNTSIVMPITRDIFYESLDSVFVSHEADMMYKTKHLQYGWCSSSLDGSGNTASKCLKFEKHLIEKKSEKKLPISAMFLKSVTELNNEISRSAXXXXXXXXXXXXXXXXXXXXXXXKSRSKLKDRKGNNIADKMPSSAQPLIHNV 1708
            MFNGNLNTSIVMPITRDIFYESLDSVFVSHEADMMYKTKHLQYGWCSSSLDGSGNTASKCLKFEKHLIEK SEKKLPISAMFLKSVTELNNEISRSAFISILVIEIVFVIVFSVLIVILIKSRSKLKDRKGNNIADKMPSSAQPLIHNV
Sbjct:    1 MFNGNLNTSIVMPITRDIFYESLDSVFVSHEADMMYKTKHLQYGWCSSSLDGSGNTASKCLKFEKHLIEKNSEKKLPISAMFLKSVTELNNEISRSAFISILVIEIVFVIVFSVLIVILIKSRSKLKDRKGNNIADKMPSSAQPLIHNV 149
The following BLAST results are available for this feature:
BLAST of SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 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 SMED30025143 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053420.13.162e-12095.53SMESG000053420.1[more]
SMESG000053420.11.521e-10891.28SMESG000053420.1[more]
SMESG000053409.13.223e-9496.48SMESG000053409.1[more]
SMESG000053409.15.273e-9496.48SMESG000053409.1[more]
SMESG000053412.14.231e-8199.33SMESG000053412.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025143 ID=SMED30025143|Name=SMED30025143|organism=Schmidtea mediterranea sexual|type=transcript|length=1840bp
ATCTAAATTATTTAATGTGTAATTGCTGCACATCAAATAATAATTCACCG
TTGCCAACAGAACGGGTATTTGGAAACAAAATGAAATTACCCGGCGACAT
AGCACTCAATGAGTGCTCTGAAACAAGAGAACTTAAAACTAATTAAAAAT
AATATCGCCGAAAAAATTCTGAGAAAAAAGAAAGACCTGAGAATGTAAAA
GTTTCAGTTCAAATAGAATTAGGTAATTGTTACAAAAACTAACAACCAAA
GAAATAGATCTTGATTTCAATCGGCCATTCAAAGTAATAAAAACAGATAA
GCAGATTTGAAAACTTACAAAATATCAATTAACGGTAGAGACAAAGTTGT
TACTTCAGATCGACTTCGTGCAACAATTGAACGGACGCATTATCTTGGAG
GGGGCAGTTATGTGGAGTTTAGTTATTATGAAATTATTTAATTTGTTTTG
TTAATAAAATAAAGTTTAAATTATGACTTCATCTTTTGAAAACAAGTCAT
TCTACAACATGTTCATTTACAATATTAATATTATTGAATTAATAAACAGA
AATGATAACTTTATAACTGGACCAGTCAGAGACAGAAGATTAAAAGATGA
GCTAACAATGAAACCAACAATGAGCACAGAAGAACCTAATCAACTGGCAA
AAATTTAGGAATAATTGCTTTCAAAAGAAAATGTTGAAGAAATTATGGTA
ATAAAACAGAAGTTACAAGAAGAAATCCTGAAATGATTACAAGAAAAACA
AATTCACGCGAGTAAAAAGATTACCCAATTCTAAAGAAAGCTGACAATGA
AACAGCAATGATATATTTGATGAATACTCCACAACACGAAGGAGGATATC
CCAATAATGACCAGTTACGGGGCTGTATTTACGATGTGAAATACAATGGC
AAATCATTAAATATGACTGCCAGTAGCAAAGAAATTGGAAATAAATGCAA
AAGGGTTTGTTTAAACGATATCTGCAACAACGGCGAGTGTTTCGAAACAT
TTTCTGACAAGCCGATATGTGATTGCAAATTGACAATGAATAACGGGCAG
TATTGCAATACAAGTTTTGTTCAAATAAATGATAGAAAACTACATGGAAA
CAAGGAAATTATCCGAATGGAACATATAAAATTGGTGTTGTTCAATAGCT
CTGATAAAGATTTGTTTCATATAAAATACGACCATTTCAAATTCCTCATA
AAACGCGAAAATTCATCACTTTTGGCAAAATATGAAGATTCAGAAAATAG
ATTGGTTGAAAATGTTCAACGGGAACCTCAATACTTCAATTGTGATGCCA
ATTACTAGAGATATCTTTTATGAGTCTTTGGATTCGGTATTCGTTTCCCA
CGAAGCTGACATGATGTATAAAACGAAACATTTGCAATATGGCTGGTGCA
GTTCTAGCTTAGACGGATCTGGAAACACTGCCAGTAAGTGTTTAAAATTT
GAAAAGCATCTTATCGAGAAAAAGTCGGAAAAAAAGTTACCAATTTCAGC
AATGTTCTTGAAGTCAGTAACTGAACTAAATAACGAAATTAGTCGATCTG
CTTTTATTAGTATTTTGGTAATAGAAATCGTCTTCGTCATTGTATTTTCT
GTTCTGATTGTCATTTTGATTAAATCCAGGAGTAAATTGAAGGACAGAAA
AGGAAATAACATAGCAGATAAAATGCCATCGAGTGCACAACCTCTCATTC
ATAACGTATAATGATAAAATTTATAAAAACATATATATTCTATAAGCCTA
CTTCCATGTTTCAATAAGTTCAATATAATGATAAAATTTATAAAAACATA
TATATTCTATAAGCCTACTTCCATGTTTCAATAAGTTCAA
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protein sequence of SMED30025143-orf-1

>SMED30025143-orf-1 ID=SMED30025143-orf-1|Name=SMED30025143-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=167bp
MIYLMNTPQHEGGYPNNDQLRGCIYDVKYNGKSLNMTASSKEIGNKCKRV
CLNDICNNGECFETFSDKPICDCKLTMNNGQYCNTSFVQINDRKLHGNKE
IIRMEHIKLVLFNSSDKDLFHIKYDHFKFLIKRENSSLLAKYEDSENRLV
ENVQREPQYFNCDANY*
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protein sequence of SMED30025143-orf-2

>SMED30025143-orf-2 ID=SMED30025143-orf-2|Name=SMED30025143-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp
MKIQKIDWLKMFNGNLNTSIVMPITRDIFYESLDSVFVSHEADMMYKTKH
LQYGWCSSSLDGSGNTASKCLKFEKHLIEKKSEKKLPISAMFLKSVTELN
NEISRSAFISILVIEIVFVIVFSVLIVILIKSRSKLKDRKGNNIADKMPS
SAQPLIHNV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR013320ConA-like_dom_sf