SMED30029462

Overview
NameSMED30029462
Smed IDSMED30029462
Length (bp)854
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 SMED30029462 (SMED30029462) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30029462 (SMED30029462) 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 SMED30029462 (SMED30029462) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30029462 (SMED30029462) 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



SMED30029462

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
nervous systemSMED30029462 dd_Smed_v4_26635_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30029462 dd_Smed_v4_26635_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30029462 dd_Smed_v4_26635_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
Alignments
SMED30029462 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001755:56158..57092 +3803
Homology
[Close]
BLAST of SMED30029462 vs. Planmine SMEST
Match: SMESG000015193.1 (SMESG000015193.1)

HSP 1 Score: 57.3806 bits (137), Expect = 3.976e-17
Identity = 35/69 (50.72%), Postives = 41/69 (59.42%), Query Frame = 2 
Query:  461 FILSESSEFLEQIXMXTASINKSLTATANQDIKTILKIF-----MNNWIYKYGKPQSILPNRM*YVESK 652
             IL ESSE LEQI M  A + +  T+T    +  I+  F     MNNWIYKYGKPQSIL +R    ESK
Sbjct:   74 LILRESSECLEQIVMDVAVMER--TSTEKMYVIVIIHRFSKLTLMNNWIYKYGKPQSILTDRGGNFESK 140

HSP 2 Score: 40.817 bits (94), Expect = 3.976e-17
Identity = 21/31 (67.74%), Postives = 23/31 (74.19%), Query Frame = 3 
Query:  294 MDKKYLAVVLLSYQSK*VIKKHEYLCHVGIK 386
            MDK  + V+  SYQSK VIK HE LCHVGIK
Sbjct:    1 MDKIDIVVIPKSYQSKLVIKTHEGLCHVGIK 31

HSP 3 Score: 27.7202 bits (60), Expect = 3.976e-17
Identity = 14/24 (58.33%), Postives = 17/24 (70.83%), Query Frame = 1 
Query:  391 KDKAKRCVTPAK*TMDQGKIKEII 462
            KD  +RCV  AK  +DQGK KEI+
Sbjct:   51 KDIVQRCVKCAKRKIDQGKTKEIL 74
[Close]
BLAST of SMED30029462 vs. Planmine SMEST
Match: SMESG000011130.1 (SMESG000011130.1)

HSP 1 Score: 56.9954 bits (136), Expect = 8.478e-10
Identity = 33/76 (43.42%), Postives = 40/76 (52.63%), Query Frame = 2 
Query:  461 FILSESSEFLEQIXMXTASINKS-------------------LTATANQDIKTILKIFMNNWIYKYGKPQSILPNR 631
             I  ESSEFLEQI M  A + ++                   LT T+ Q+  T+ K  MNNWIYKYGKP+SIL  R
Sbjct:   50 LIPCESSEFLEQIVMDVAVMERTSTDEKYVIVIIDRFSKLVCLTTTSKQNEPTLWKTLMNNWIYKYGKPKSILMER 125
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BLAST of SMED30029462 vs. Planmine SMEST
Match: SMESG000045039.1 (SMESG000045039.1)

HSP 1 Score: 56.225 bits (134), Expect = 2.771e-9
Identity = 30/42 (71.43%), Postives = 31/42 (73.81%), Query Frame = 2 
Query:  527 SLTATANQDIKTILKIFMNNWIYKYGKPQSILPNRM*YVESK 652
            SLTAT NQD KTI K  MNNWIYKY KPQSIL +R    ESK
Sbjct:   23 SLTATPNQDEKTIWKRLMNNWIYKYCKPQSILMDRGRNFESK 64
[Close]
BLAST of SMED30029462 vs. Planmine SMEST
Match: SMESG000078347.1 (SMESG000078347.1)

HSP 1 Score: 42.3578 bits (98), Expect = 4.231e-9
Identity = 22/35 (62.86%), Postives = 27/35 (77.14%), Query Frame = 3 
Query:  282 VALQMDKKYLAVVLLSYQSK*VIKKHEYLCHVGIK 386
            +A++MDK  L V+  S+QSK VIK HE LCHVGIK
Sbjct:  308 LAMEMDKIDLVVIPKSHQSKLVIKIHEDLCHVGIK 342

HSP 2 Score: 28.8758 bits (63), Expect = 4.231e-9
Identity = 15/24 (62.50%), Postives = 18/24 (75.00%), Query Frame = 1 
Query:  391 KDKAKRCVTPAK*TMDQGKIKEII 462
            K+  KRCVT AK  + QGKIKEI+
Sbjct:  362 KNIVKRCVTCAKRKIYQGKIKEIL 385

HSP 3 Score: 26.5646 bits (57), Expect = 4.231e-9
Identity = 14/28 (50.00%), Postives = 19/28 (67.86%), Query Frame = 2 
Query:  452 KK*FILSESSEFLEQIXMXTASINKSLT 535
            K+  IL ESSEFL+QI M  A + ++ T
Sbjct:  382 KEILILRESSEFLKQIVMDVAIMERTST 409
[Close]
BLAST of SMED30029462 vs. Planmine SMEST
Match: SMESG000078347.1 (SMESG000078347.1)

HSP 1 Score: 42.3578 bits (98), Expect = 4.438e-9
Identity = 22/35 (62.86%), Postives = 27/35 (77.14%), Query Frame = 3 
Query:  282 VALQMDKKYLAVVLLSYQSK*VIKKHEYLCHVGIK 386
            +A++MDK  L V+  S+QSK VIK HE LCHVGIK
Sbjct:  307 LAMEMDKIDLVVIPKSHQSKLVIKIHEDLCHVGIK 341

HSP 2 Score: 28.8758 bits (63), Expect = 4.438e-9
Identity = 15/24 (62.50%), Postives = 18/24 (75.00%), Query Frame = 1 
Query:  391 KDKAKRCVTPAK*TMDQGKIKEII 462
            K+  KRCVT AK  + QGKIKEI+
Sbjct:  361 KNIVKRCVTCAKRKIYQGKIKEIL 384

HSP 3 Score: 26.5646 bits (57), Expect = 4.438e-9
Identity = 14/28 (50.00%), Postives = 19/28 (67.86%), Query Frame = 2 
Query:  452 KK*FILSESSEFLEQIXMXTASINKSLT 535
            K+  IL ESSEFL+QI M  A + ++ T
Sbjct:  381 KEILILRESSEFLKQIVMDVAIMERTST 408
The following BLAST results are available for this feature:
BLAST of SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 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 SMED30029462 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015193.13.976e-1750.72SMESG000015193.1[more]
SMESG000011130.18.478e-1043.42SMESG000011130.1[more]
SMESG000045039.12.771e-971.43SMESG000045039.1[more]
SMESG000078347.14.231e-962.86SMESG000078347.1[more]
SMESG000078347.14.438e-962.86SMESG000078347.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30029462 ID=SMED30029462|Name=SMED30029462|organism=Schmidtea mediterranea sexual|type=transcript|length=854bp
TAAAAATATTTTTTTGTGTGCATTTTGTCAAAAATTGAAAATGGACGAAT
TATAAGCGCCACTTTAGAATTTTAAAATATCTCAGTTATTTCAGAGGATA
TCCATGGATGTAACTGGGCCCATACAAAAAACTACACGAAAAAACAAATA
TATTATTGGGGGACCAATGGAGTCAATGGTTCACAAACTTGAATGCCCAG
GTTATGTTCATTCTCAATAACGGTTGCAATTTTCAGAGTTAGCTATTTGC
GGTTTTAATATGATCATAGAAGTAAAACAAAGTTGCATTGCAAATGGACA
AAAAATATCTAGCGGTAGTCCTACTAAGCTATCAATCTAAATGAGTGATT
AAAAAACATGAATATTTATGTCATGTTGGAATTAAGATAAAAAGATAAAG
CAAAACGATGTGTCACGCCTGCAAAATGAACAATGGACCAAGGAAAGATA
AAAGAAATAATTTATTTTATCCGAAAGTTCTGAATTTCTAGAACAGATTG
NTATGGANACAGCTTCAATCAACAAAAGTCTAACGGCCACAGCAAACCAA
GATATTAAAACTATTTTGAAGATCTTCATGAACAACTGGATTTACAAATA
CGGTAAACCTCAAAGTATATTGCCGAACAGAATGTAATATGTTGAAAGTA
AATAAGAAGATGGATATGTCAGCTCCAGGACGCCCATTCTATAAATTTTC
CAGAAGATGGGCAAGTTTTTGTAGGTCACGAAATATATATTTTATATAGG
TAGCATATATACTGTTCCCAGGAAGCCATTCAAAATTAAGNNNNTNGAGT
GTAGGTTGCAAGAAATTAAATTCAAGCCTATTAAATCTGACCAATATACA
AGCG
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