SMED30017298

Overview
NameSMED30017298
Smed IDSMED30017298
Length (bp)1071
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 SMED30017298 (SMED30017298) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017298 (SMED30017298) 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 SMED30017298 (SMED30017298) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017298 (SMED30017298) 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



SMED30017298

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
anterior region of the whole animalSMED30017298 dd_Smed_v4_17790_0_2dd_Smed_v4PMID:27063937
Scimone et al., 2016		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynxSMED30017298 dd_Smed_v4_17790_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30017298 dd_Smed_v4_17790_0_2dd_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 SMED30017298 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 117.472 bits (293), Expect = 9.734e-45
Identity = 54/84 (64.29%), Postives = 67/84 (79.76%), Query Frame = 2 
Query:  470 NNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQ 721
            ++SWIDASR+  RFP  +AARCRQAMWD  FSI PVRE+R   Q D++E++L +VAIK EPGR+P RE R +AE+ LARLERHQ
Sbjct:   89 HDSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRSPAREMRGQAEYLLARLERHQ 172

HSP 2 Score: 82.0333 bits (201), Expect = 9.734e-45
Identity = 46/84 (54.76%), Postives = 59/84 (70.24%), Query Frame = 1 
Query:  721 AKTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQ-DYDGQPPQRQEHSYA 969
            A+TN QV  AR+ L RVN+DIA G+IPST GYA +Y VS+ELDDP L    + M V + R +LP+E++ + D   PQR EHSYA
Sbjct:  173 AETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQR-EHSYA 255
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BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1)

HSP 1 Score: 119.783 bits (299), Expect = 1.385e-43
Identity = 53/87 (60.92%), Postives = 72/87 (82.76%), Query Frame = 2 
Query:  467 ENNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727
            +++SWIDASR+T+RFP ++ ARCRQ +WD  FS+SPVRESR + + D+++++LP VAIK EPGRNP RE R +AEF LARLE HQ++
Sbjct:  358 DDHSWIDASRVTVRFPARSVARCRQVLWDAGFSVSPVRESRTATRRDDEKVDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQ 444

HSP 2 Score: 75.8702 bits (185), Expect = 1.385e-43
Identity = 42/82 (51.22%), Postives = 52/82 (63.41%), Query Frame = 1 
Query:  724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA 969
            +T  QV  ARR L  +N+ IATG IPST  YA  Y VS+ LDDP L      M+VV+ R +L RE++D D +  Q QEHSYA
Sbjct:  444 QTKRQVNRARRHLAEINKAIATGDIPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVPRRILTREMKDKDRRSNQDQEHSYA 525
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BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000030287.1 (SMESG000030287.1)

HSP 1 Score: 118.627 bits (296), Expect = 9.034e-42
Identity = 55/86 (63.95%), Postives = 70/86 (81.40%), Query Frame = 2 
Query:  470 NNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727
            ++SWIDASR+T+RFP ++AARCRQA+WD  FS+SPVRESR     +++E+EL  VAIK EPGRNP RE R +AEF LARLE HQ++
Sbjct:  306 DHSWIDASRVTVRFPARSAARCRQALWDLGFSVSPVRESRVGTYREDEEVELLFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQ 391

HSP 2 Score: 70.8626 bits (172), Expect = 9.034e-42
Identity = 40/82 (48.78%), Postives = 49/82 (59.76%), Query Frame = 1 
Query:  724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA 969
            + N QV  +RR L  +N+ IATG IPST  YA+ Y VSY LDDP L      M+VV+     PR +   D +P Q QEHSYA
Sbjct:  391 QNNRQVDRSRRHLAEINKAIATGDIPSTDWYALPYNVSYNLDDPNLAGETEAMNVVV-----PRRMLAADRRPYQDQEHSYA 467
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BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000031752.1 (SMESG000031752.1)

HSP 1 Score: 107.071 bits (266), Expect = 5.483e-41
Identity = 54/93 (58.06%), Postives = 68/93 (73.12%), Query Frame = 1 
Query:  724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA*NQSGWSSNPR 1002
            +TNWQV +ARRR++RV  DIA G+IPST G+  +YGVSYELDD  L EMD P+DVV+ R L+P  + D + + PQRQEHSYA N+    SN R
Sbjct:   81 QTNWQVLVARRRMDRVKADIAAGRIPSTDGHTSEYGVSYELDDLALKEMDAPIDVVVPRRLIPSNILDRNRRSPQRQEHSYARNRPVNPSNFR 173

HSP 2 Score: 80.1073 bits (196), Expect = 5.483e-41
Identity = 41/67 (61.19%), Postives = 50/67 (74.63%), Query Frame = 2 
Query:  527 ARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727
            ARC QAMWD  +SIS V+ESRE     +DE+EL +VA+K EP RN  REAR RAEFTL RLE H+++
Sbjct:   15 ARCWQAMWDAGYSISTVKESREHHLSRHDEVELAYVAMKREPVRNLAREARQRAEFTLIRLEIHKRQ 81
[Close]
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000038895.1 (SMESG000038895.1)

HSP 1 Score: 107.457 bits (267), Expect = 2.376e-40
Identity = 57/100 (57.00%), Postives = 71/100 (71.00%), Query Frame = 1 
Query:  724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA*NQSGWSSNPRVESHPRR 1023
            +TNWQVAM R R +RVN +IATG+IPST GY   Y VSYEL+DP L EMD PMDVV+ R LLP  + + + + PQRQEHSYA ++  + SN R  +  RR
Sbjct:   65 QTNWQVAMVRNRSDRVNAEIATGRIPSTDGYIPGYRVSYELNDPALEEMDAPMDVVVPRRLLPSNILERNRRSPQRQEHSYACSRPVYPSNSRNINRQRR 164

HSP 2 Score: 77.411 bits (189), Expect = 2.376e-40
Identity = 40/63 (63.49%), Postives = 48/63 (76.19%), Query Frame = 2 
Query:  539 QAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727
            +AMWD  +SIS VRES + R   NDE+EL +VAIK EP RNPV EA  RAEFTLARL+ HQ++
Sbjct:    3 EAMWDAGYSISSVRESMDHRLSRNDEVELSYVAIKREPWRNPVIEAGQRAEFTLARLDIHQRQ 65
The following BLAST results are available for this feature:
BLAST of SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 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 SMED30017298 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013157.19.734e-4564.29SMESG000013157.1[more]
SMESG000023390.11.385e-4360.92SMESG000023390.1[more]
SMESG000030287.19.034e-4263.95SMESG000030287.1[more]
SMESG000031752.15.483e-4158.06SMESG000031752.1[more]
SMESG000038895.12.376e-4057.00SMESG000038895.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017298 ID=SMED30017298|Name=SMED30017298|organism=Schmidtea mediterranea sexual|type=transcript|length=1071bp
AAATAAATGAAACCGTGTTTTGAAATTCAGCAAATATAAATAATGTTAGT
ATTTTGAAATCCGTGAAAATGCGGTGAGAACAACGAGCACATGATTAGTG
ATTCAACGACGTCATGACACGTCAACAATATTAGTGTGGCAGCGCAAAAA
ATTAAATTCGAGGTGTGCCAGAATTTCTACAAAAAATGATAGCGAGATAG
AAAATAAAAATGTAAAGCTAAACCAGTGGAAGGAAAATTATCGATTAATA
ATGACTAAATACCACACCAACAAAGACAGGTATATATCGCCGATCACCGG
AGGAATCAATCAGTTTGACAAAACTGAACTTTAGGAAAAGAAAATGATCA
CACCAAGGGATTTCATAATAATGACTAAGAAGACGAGCGATGAAAACCAA
AATGGCCCCAATGTCAAACAACGAGGTGAAACCAGAAAGAGGGAACTACT
GAGGAGGAAAGAGGACGAAAACAACTCCTGGATCGACGCATCCAGGATCA
CCTTGAGATTTCCGGTGCAAACGGCTGCGCGATGCCGACAAGCAATGTGG
GACACCAGTTTCTCCATCTCCCCGGTACGAGAATCAAGAGAGAGCCGACA
ATTCGACAATGATGAGATGGAGCTGCCTCATGTAGCCATAAAGAGCGAGC
CTGGACGAAATCCAGTACGGGAAGCCCGATAGAGAGCCGAGTTCACATTA
GCTCGACTGGAAAGACATCAGCAAAAACAAATTGGCAAGTCGCAATGGCT
AGACGACGCCTGAACAGGGTGAATCAAGATATCGCAACAGGAAAAATTCC
AAGCACCGTCGGCTATGCCATAAAATACGGAGTATCCTATGAGCTCGATG
ACCCAGTTCTGGTGGAGATGGATACTCCAATGGATGTCGTGATCCTGAGA
TGACTACTGCCAAGAGAACTGCAGGACTATGACGGCCAACCACCTCAGCG
GCAAGAACATTCCTACGCTTAAAATCAATCTGGGTGGTCATCAAACCCTC
GTGTCGAAAGCCACCCAAGGAGATGAGGAGTTCAGTAGTTAATAATCTGG
AAAAAATACAAACTATAGAAT
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protein sequence of SMED30017298-orf-1

>SMED30017298-orf-1 ID=SMED30017298-orf-1|Name=SMED30017298-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MITPRDFIIMTKKTSDENQNGPNVKQRGETRKRELLRRKEDENNSWIDAS
RITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIK
SEPGRNPVREAR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000140anterior region of the whole animal