SMED30029256

Overview
NameSMED30029256
Smed IDSMED30029256
Length (bp)1807
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 SMED30029256 (SMED30029256) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029256 (SMED30029256) 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 SMED30029256 (SMED30029256) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029256 (SMED30029256) 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



SMED30029256

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
posterior sideSMED30029256SMESG000027017.1 dd_Smed_v4_7351_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30029256SMESG000027017.1 dd_Smed_v4_7351_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30029256SMESG000027017.1 dd_Smed_v4_7351_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 SMED30029256 vs. Planmine SMEST
Match: SMESG000027017.1 (SMESG000027017.1)

HSP 1 Score: 452.595 bits (1163), Expect = 2.874e-158
Identity = 221/227 (97.36%), Postives = 224/227 (98.68%), Query Frame = 3 
Query:  102 MNTAISKAVVPLVPNGEYTQINYFQNTSESEKESKFCELQQKSTDINLNLHKLILKQEDEIHKLKGRIESLISLFNKKQEAVEKTLVSLQSQIQKTKEEIKNLKPGELSWEIYVLRDQHSDSFFSSENGYKMRLKMQVKRFIVESYLFFKLEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTFIDYNWFSKFWFNDMMLVKCFVN 782
            MNTAISKAVVPLVPNGEYTQINYFQNTSESEKESKFCELQQKSTDINLNLHKLILKQEDEIHKLKGRIESLISLFN KQEA+EKTLVSLQSQIQKTKEEIKNLKPGELSWEIYVLRDQ SDSFFSSENGYKMRLKM VKRFIVESYL+FKLEMAQTANNNNLQWPNEFD+RVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTFIDYNWFSKFWFNDMMLVKCFVN
Sbjct:    1 MNTAISKAVVPLVPNGEYTQINYFQNTSESEKESKFCELQQKSTDINLNLHKLILKQEDEIHKLKGRIESLISLFNIKQEAIEKTLVSLQSQIQKTKEEIKNLKPGELSWEIYVLRDQDSDSFFSSENGYKMRLKMHVKRFIVESYLYFKLEMAQTANNNNLQWPNEFDIRVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTFIDYNWFSKFWFNDMMLVKCFVN 227
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BLAST of SMED30029256 vs. Planmine SMEST
Match: SMESG000027028.1 (SMESG000027028.1)

HSP 1 Score: 114.005 bits (284), Expect = 1.846e-28
Identity = 70/198 (35.35%), Postives = 116/198 (58.59%), Query Frame = 3 
Query:  213 ELQQKSTDINLNLHKLILKQE----DEIHKLKGRIESLISLFNKKQEAVEKT---LVSLQSQIQK----TKEEIKNLKPGELSWEIYVLRDQHSDSFFSSENGYKMRLKMQVKRFIVESYLFFKLEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTFIDYNWFSKFWFNDMMLVKC 773
            E QQKS +I+L L  +IL Q+     + +++  ++ S+ +  NK Q  V +      +L+++I+K    T++ I+  K G   W I  L DQ SD F+S ENG+KMRL++  ++ I+ + +   L++A+  +N NL +P EFDVR+G VN +   F  S+KQVILF+ P S+H+  F F  ++     W    +++KC
Sbjct:   30 EYQQKSNEISLKLQNMILDQDKASKSKSNEMDMKLNSMKTSINKIQSEVNEMKNKFRTLENEIKKLHDTTEKNIQRYKSGNFLWTISSLSDQVSDPFYSHENGFKMRLELFREQNILFNGIHIFLKLAKVHSNTNLHFPVEFDVRIGTVNPTTNAFFTSQKQVILFENPDSLHKKPFCFSYFDVSGYSWSKCDLIIKC 227
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BLAST of SMED30029256 vs. Planmine SMEST
Match: SMESG000027028.1 (SMESG000027028.1)

HSP 1 Score: 110.153 bits (274), Expect = 4.552e-27
Identity = 67/179 (37.43%), Postives = 108/179 (60.34%), Query Frame = 3 
Query:  213 ELQQKSTDINLNLHKLILKQE----DEIHKLKGRIESLISLFNKKQEAVEKT---LVSLQSQIQK----TKEEIKNLKPGELSWEIYVLRDQHSDSFFSSENGYKMRLKMQVKRFIVESYLFFKLEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTF 716
            E QQKS +I+L L  +IL Q+     + +++  ++ S+ +  NK Q  V +      +L+++I+K    T++ I+  K G   W I  L DQ SD F+S ENG+KMRL++  ++ I+ + +   L++A+  +N NL +P EFDVR+G VN +   F  S+KQVILF+ P S+H+  F F
Sbjct:   30 EYQQKSNEISLKLQNMILDQDKASKSKSNEMDMKLNSMKTSINKIQSEVNEMKNKFRTLENEIKKLHDTTEKNIQRYKSGNFLWTISSLSDQVSDPFYSHENGFKMRLELFREQNILFNGIHIFLKLAKVHSNTNLHFPVEFDVRIGTVNPTTNAFFTSQKQVILFENPDSLHKKPFCF 208
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BLAST of SMED30029256 vs. Planmine SMEST
Match: SMESG000027039.1 (SMESG000027039.1)

HSP 1 Score: 95.1301 bits (235), Expect = 2.017e-23
Identity = 44/96 (45.83%), Postives = 64/96 (66.67%), Query Frame = 3 
Query:  495 MRLKMQVKRFIVESYLFFKLEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHETSFTFIDYNWFSKFWFNDMMLVKCFVN 782
            MRL++  +R+ +   +   ++M Q AN+ NLQWP EFD+R+GIVNQ NG+F  SEKQ+ILF+   S HE+ F F  Y+     W N+ +++KC VN
Sbjct:    1 MRLQLVPERYWIRQGISVIVKMVQGANDKNLQWPVEFDIRIGIVNQENGQFFRSEKQIILFKNSTSTHESPFKFSPYDLSGSAWKNNRLVIKCCVN 96
[Close]
BLAST of SMED30029256 vs. Planmine SMEST
Match: SMESG000049695.1 (SMESG000049695.1)

HSP 1 Score: 55.0694 bits (131), Expect = 1.683e-8
Identity = 36/117 (30.77%), Postives = 57/117 (48.72%), Query Frame = 3 
Query:  375 QIQKTKEEIKNLKPGELSWEIYVLRDQ------HSDSFFSSENGYKMRLKMQVKRFIVESYLFFKLEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHETS 707
            QIQ T  +   LK G   WEI  + +Q      +S  F+S   GYKM L + +     + Y+     + +   +NNL+WP ++ V V +++ +NG  +I  K V    CP +  E S
Sbjct:   69 QIQSTFGDENLLKSGFFEWEIDKISEQRREELIYSKPFYSGPFGYKMCLAVFIGG---DDYIDVYFHLMRGGFDNNLEWPFKYSVAVDVIDSANGN-IIDSKSVKYSNCPDAADEAS 181
The following BLAST results are available for this feature:
BLAST of SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 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 SMED30029256 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000027017.12.874e-15897.36SMESG000027017.1[more]
SMESG000027028.11.846e-2835.35SMESG000027028.1[more]
SMESG000027028.14.552e-2737.43SMESG000027028.1[more]
SMESG000027039.12.017e-2345.83SMESG000027039.1[more]
SMESG000049695.11.683e-830.77SMESG000049695.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029256 ID=SMED30029256|Name=SMED30029256|organism=Schmidtea mediterranea sexual|type=transcript|length=1807bp
CTTTGTTCAAGGTTGAAGCCTTTTCTTAGAATTAATTATAATTTTCATGA
AAAGAAACTCTGAATCTAAAATATTTCAAAAATAAACAATCAGTTTTACT
AATGAATACCGCAATATCAAAAGCCGTTGTTCCATTAGTGCCAAATGGAG
AATATACACAAATAAATTACTTCCAAAATACTTCAGAATCCGAAAAAGAA
TCCAAGTTTTGCGAACTTCAACAAAAATCAACAGACATCAATCTTAATCT
TCACAAGTTGATTTTAAAGCAGGAGGATGAAATTCATAAATTAAAAGGTC
GCATAGAATCACTTATTAGCTTATTCAATAAAAAACAAGAGGCAGTAGAA
AAAACTCTCGTAAGTCTCCAAAGCCAAATACAAAAAACAAAAGAAGAAAT
AAAAAACCTAAAGCCAGGAGAACTATCCTGGGAAATATATGTTTTGAGAG
ACCAACATAGTGATTCGTTTTTCAGTAGTGAAAATGGCTATAAAATGCGC
CTTAAAATGCAAGTGAAGCGATTTATAGTAGAGTCTTATTTGTTTTTCAA
GCTTGAAATGGCACAAACTGCAAATAACAATAATTTACAATGGCCAAATG
AATTCGATGTCCGAGTTGGGATTGTCAATCAGTCAAATGGAAAATTCCTT
ATATCAGAGAAGCAGGTTATCCTATTTCAATGCCCCAAGTCCATTCACGA
GACCTCGTTCACATTTATTGACTATAATTGGTTTAGTAAATTCTGGTTCA
ATGATATGATGCTAGTCAAATGCTTTGTCAATTGATCAGGTTGTCTTGAT
CTCCTCGATTTTCTTTATCCGAAACTATTATTAGGTTATGATACATATAT
TAATTTATTCTTTTGATTTAGTTAATTTTGTTGGGTTATTAATATTTGTC
GGTGATTATTAAATTACCAATTACAGATCTGACTCCGAGCGTGTCTTATT
AATAACTATATTGACGAATTCCAACTACGTAAAACTTTTTTGATTATCAC
AATTGATTACAACAATTATATGTTAATTTCAACACACTTCAAATGCTTCT
GGCGCTTATTACAACCTTTCGGGAGGGATAGCACAACACCATACCCTGAT
CACACGACCACTTGACTACTACTGATGACAGGTAACATAATACAATTGAT
TTGGTTGCCTTTTTAGCTTGATCAGGATTCTTCTGATTATTATATCGATT
TCCAACACTTTATAAATTCAGTACCCTTGTTTCAATTTCCAGTAATTTAT
CCTTTTTAATTTCTTCTCCCTTCTATTTTTCCTGTGCCTTATACTCGCTT
GTGTCTAGATTTTATACTTTTCCGTCTTATTTACCAACTTGTTCCATTGA
GTACTCTGTAATCTCTGACAACTGTCGAGGTATACATTTTTTGACAATAC
CATTTCTCGGCTTCCCAATATCATTTTTTTCTTTATCTCGAATATGTTAT
CGAGATAACAAGATAATTTTAACTTTGTTTTTGTTTTTCTTCTTTTGAAC
TTGTACTTATTAATTTGGAATGACCTTTTATTCAACTGTTTGCTTTTATT
GATTTTCTTCTATTCCCTTCTCATTTTTCGATCTCTTTTCCACTCCTATT
TTACTGAGTTCCAGAACAATACATCATTCATTTATCATCACCACCCCCAC
GCATTTAATAATTATTTTTGTTTTATTATTTGGGTATCCTCAACAGAATA
TACAAACGCTTATTCAACATCATTTTGTTGATCATCTTAGACTGAAGTAA
TTGATTAATATTTGTGTTCGTATTGCCGCATTTTCAGTGTAATATGGTTT
ATGCAAA
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protein sequence of SMED30029256-orf-1

>SMED30029256-orf-1 ID=SMED30029256-orf-1|Name=SMED30029256-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=228bp
MNTAISKAVVPLVPNGEYTQINYFQNTSESEKESKFCELQQKSTDINLNL
HKLILKQEDEIHKLKGRIESLISLFNKKQEAVEKTLVSLQSQIQKTKEEI
KNLKPGELSWEIYVLRDQHSDSFFSSENGYKMRLKMQVKRFIVESYLFFK
LEMAQTANNNNLQWPNEFDVRVGIVNQSNGKFLISEKQVILFQCPKSIHE
TSFTFIDYNWFSKFWFNDMMLVKCFVN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR008974TRAF-like
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding