SMED30022699

Overview
NameSMED30022699
Smed IDSMED30022699
Length (bp)1946
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 SMED30022699 (SMED30022699) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022699 (SMED30022699) 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 SMED30022699 (SMED30022699) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022699 (SMED30022699) 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




SMED30022699

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
protonephridiaSMED30022699SMESG000056221.1 SMESG000046858.1 SMESG000029613.1 SMESG000025472.1 SMESG000023703.1 SMESG000011090.1 dd_Smed_v4_17710_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30022699SMESG000056221.1 SMESG000046858.1 SMESG000029613.1 SMESG000025472.1 SMESG000023703.1 SMESG000011090.1 dd_Smed_v4_17710_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022699 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001439:76969..78812 +4410
Homology
BLAST of SMED30022699 vs. Planmine SMEST
Match: SMESG000025472.1 (SMESG000025472.1)

HSP 1 Score: 199.519 bits (506), Expect = 8.785e-91
Identity = 95/109 (87.16%), Postives = 101/109 (92.66%), Query Frame = 2
Query: 1118 FRHACFGEVVEGMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLE 1444
             +HA FGEVVEG++IN NFSSDIE+YFEKQHSF DF NAEENLVTEN TEQEVE NLSLSDTS+NNQCVKLPNIHKAFECMQQVV+FYSN DKTDHLQESLIAIESDLE
Sbjct:   93 LKHAGFGEVVEGLSINENFSSDIEKYFEKQHSFIDFVNAEENLVTENFTEQEVELNLSLSDTSENNQCVKLPNIHKAFECMQQVVLFYSNQDKTDHLQESLIAIESDLE 201          

HSP 2 Score: 154.836 bits (390), Expect = 8.785e-91
Identity = 80/86 (93.02%), Postives = 81/86 (94.19%), Query Frame = 3
Query:  849 I*TLKQKFEIIALFEKG*SQASLVRKYKISPSSISNICHKKREEILEAYSSRPSSTKKLKQSFYDDLDIQLRDWYLLQRSKK*KIP 1106
            I TLKQKFEIIALFEKG SQASLV KYKISPSSISNICHKKREEILEAYSSRPSSTKKLKQSFYDDL+IQLRDWYLLQRSK  KIP
Sbjct:    8 ILTLKQKFEIIALFEKGESQASLVSKYKISPSSISNICHKKREEILEAYSSRPSSTKKLKQSFYDDLNIQLRDWYLLQRSK--KIP 91          
BLAST of SMED30022699 vs. Planmine SMEST
Match: SMESG000056221.1 (SMESG000056221.1)

HSP 1 Score: 228.409 bits (581), Expect = 4.010e-87
Identity = 125/127 (98.43%), Postives = 125/127 (98.43%), Query Frame = 2
Query: 1124 HACFGEVVEGMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLEXXXXXXXXXXXXXXEFILKK 1504
            HACFGEVVE MAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLEKILLKK TKQRKITEFILKK
Sbjct:  276 HACFGEVVERMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLEKILLKKTTKQRKITEFILKK 402          

HSP 2 Score: 114.005 bits (284), Expect = 4.010e-87
Identity = 55/60 (91.67%), Postives = 57/60 (95.00%), Query Frame = 3
Query:  894 KG*SQASLVRKYKISPSSISNICHKKREEILEAYSSRPSSTKKLKQSFYDDLDIQLRDWY 1073
            +G SQASL RKYKISPSSISNICHKKREEILEAYSS PSSTKKLKQSFYDDLDIQLRDW+
Sbjct:  217 EGESQASLARKYKISPSSISNICHKKREEILEAYSSWPSSTKKLKQSFYDDLDIQLRDWH 276          
BLAST of SMED30022699 vs. Planmine SMEST
Match: SMESG000046858.1 (SMESG000046858.1)

HSP 1 Score: 230.335 bits (586), Expect = 1.975e-72
Identity = 130/135 (96.30%), Postives = 130/135 (96.30%), Query Frame = 2
Query: 1100 NTIKNCFRHACFGEVVEGMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLEXXXXXXXXXXXXXXEFILKK 1504
            NTIKNCFRHA FGEVVEGMAIN NFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVE NLSLSDTSDNNQCVKLPNIHKAFECMQQVV FYSN DKTDHLQESLIAIESDLEKILLKKKTKQRKITEFILKK
Sbjct:   12 NTIKNCFRHAGFGEVVEGMAINENFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVELNLSLSDTSDNNQCVKLPNIHKAFECMQQVVFFYSNQDKTDHLQESLIAIESDLEKILLKKKTKQRKITEFILKK 146          
BLAST of SMED30022699 vs. Planmine SMEST
Match: SMESG000029613.1 (SMESG000029613.1)

HSP 1 Score: 217.624 bits (553), Expect = 7.033e-68
Identity = 106/114 (92.98%), Postives = 109/114 (95.61%), Query Frame = 2
Query: 1100 NTIKNCFRHACFGEVVEGMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDL 1441
            NTIKNCFRHA FGEVVEGMAIN NFSSDIE+YFEKQHSFTDF NAEENLVTENVTEQEVE NLSLSDTSDNNQC+KLPNIHKAFECMQQVV+FYSNHDKTDHLQESLIAIESD 
Sbjct:   12 NTIKNCFRHAGFGEVVEGMAINENFSSDIEKYFEKQHSFTDFVNAEENLVTENVTEQEVELNLSLSDTSDNNQCLKLPNIHKAFECMQQVVLFYSNHDKTDHLQESLIAIESDF 125          
BLAST of SMED30022699 vs. Planmine SMEST
Match: SMESG000023703.1 (SMESG000023703.1)

HSP 1 Score: 174.096 bits (440), Expect = 1.698e-51
Identity = 85/93 (91.40%), Postives = 86/93 (92.47%), Query Frame = 2
Query: 1100 NTIKNCFRHACFGEVVEGMAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDTSDNNQCVKLPNIHKAFECMQQVVIF 1378
            NT KNCFRHA FGEVVEGMAIN NFSSDIE+YFEKQHSFTDF NAEENLVTENVTEQEVE NLSLSDTSDNNQCVKLP IHKAFECMQQVV F
Sbjct:   12 NTKKNCFRHAGFGEVVEGMAINENFSSDIEKYFEKQHSFTDFVNAEENLVTENVTEQEVELNLSLSDTSDNNQCVKLPKIHKAFECMQQVVFF 104          
The following BLAST results are available for this feature:
BLAST of SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 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 SMED30022699 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025472.18.785e-9187.16SMESG000025472.1[more]
SMESG000056221.14.010e-8798.43SMESG000056221.1[more]
SMESG000046858.11.975e-7296.30SMESG000046858.1[more]
SMESG000029613.17.033e-6892.98SMESG000029613.1[more]
SMESG000023703.11.698e-5191.40SMESG000023703.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022699 ID=SMED30022699|Name=SMED30022699|organism=Schmidtea mediterranea sexual|type=transcript|length=1946bp
CGTCCTATGACGGATAGAATAAGGGATGGGTAAACGTCTGGTTTATTTAC
ACTTTATTCAGTATAACTGTAAATAAAATAATTATTAACTTCACATTCAT
AGAAATACAAATTTATGAATTCACCCACCTCAAATGATAATATTAATCCC
GTGCATTATATATGATTACACTTTATATTAATAAAGGATGAATTTAAGAA
TTTTTGTTATTTATTTCAAGAGCTTGTAACTCGCTCGAGGTTTAAAATTG
GGCTGTCTTCATACTTACCAATTTTTATGATTTGAAGTCTTGATATAGTA
GTTTGAAATTTCGTTTTTTAAAATTATTATCTCAACTGGTTATCAGCCAA
CAACATGGGTTGAAAAAACCCGACAATTTATAACCTGCTAAGAAATTAGT
TTTGAAATTTTTGCTATTGAAACAGGCCAAAAGAGAAATATATTATTCCA
TTACGAAACTTTTCTTTGCTATCTGTATGGATTTTCTGGCATAGAAACTA
TCTGATTTTTCAAAACCTTTTAATATTTGCGTTTTAAGGATATATATGGG
AAAGAGGTATACCTGGACATAACAATAATGATGATGCATTATATCAATTA
TATGGATGAACTGGCTAAATTAAATTAGTTGTTTAAGTCTAAAAACACTT
ACAACTTACATTAAAACACAATATTTTCAAAAAAACCCACCTTCCTCAAA
AAATGGGAGATAATAAACCAAACTATGCCCACAGGCTTCCCATTTTAATA
CTAAATACCTATGCAAAATTTAATGGCTTGTCTTAAACTGTCTGGAAGAT
AAACCCAAAAATCTATAGCGTTCCAGAGTCAGTCAGTGATGAGTGTAAAT
TTAAACACTAAAACAGAAATTTGAAATCATAGCACTTTTTGAGAAAGGAT
AAAGTCAAGCATCATTGGTCAGAAAATATAAAATATCTCCTTCATCAATA
TCAAACATTTGTCACAAGAAAAGGGAAGAAATACTTGAGGCCTACAGTTC
CAGGCCTTCATCAACCAAGAAACTGAAACAATCTTTTTATGATGATTTAG
ATATTCAGTTAAGGGATTGGTATTTGCTGCAACGATCTAAAAAGTAAAAA
ATACCATAAAAAATTGTTTTAGGCATGCTTGTTTCGGCGAAGTGGTTGAA
GGAATGGCAATAAATGGAAATTTTTCATCTGATATAGAGGAATATTTTGA
AAAGCAACACTCGTTTACTGATTTTGCTAATGCTGAAGAAAATTTAGTAA
CAGAAAATGTCACTGAACAGGAAGTAGAATTTAATTTATCGCTATCTGAT
ACGTCAGATAACAATCAATGTGTTAAGCTTCCCAACATTCATAAAGCATT
TGAGTGCATGCAACAAGTAGTTATTTTTTATTCAAATCACGATAAAACTG
ACCATTTACAAGAAAGTTTAATAGCAATTGAATCAGATTTGGAGAAGATT
TTACTCAAGAAAAAAACCAAGCAGCGGAAAATAACTGAGTTTATTTTAAA
AAAATAAATGTGTTGATTAGTAAAGTTTTTTTTGATATTTTTTAAAATTA
TCCTTATAAAAAAGTATCTGTTAAAGAGAAGTATCGGTTTGCATAACTCT
AAAACAAAAATGATTATTTTCCTAACCCAGCGAGTTAATGGCGAAGTTAC
ACCGAAAATCGATTCTAATCAAAGGGATGCACCTTTCGATCATTGAATAC
CCAGTTATCTTACAGAAAGTGCTACAGTAAAAAAATTAACCAATTAATCT
CGGAAGTATCGTCAGAAGTTTAAAAAATTATCGATTCAATCAGAAATTCT
AAGTGAAATAAAATATTGCGATTAAGGAGGATTTTGCGGGCAGATTTTGT
AAGCTCATTACAATGTCTTATTAATAATGCCTCTAAATTGGGTAGAATCA
GAGCGAATTTTCTCTGCTGCTGGAGCTTTTTCGACAAAAATTCGAA
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protein sequence of SMED30022699-orf-1

>SMED30022699-orf-1 ID=SMED30022699-orf-1|Name=SMED30022699-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MAINGNFSSDIEEYFEKQHSFTDFANAEENLVTENVTEQEVEFNLSLSDT
SDNNQCVKLPNIHKAFECMQQVVIFYSNHDKTDHLQESLIAIESDLEKIL
LKKKTKQRKITEFILKK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR009057Homeobox-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding