SMED30030912

Overview
NameSMED30030912
Smed IDSMED30030912
Length (bp)604
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30030912 (SMED30030912) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030912 (SMED30030912) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30030912

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30030912 SmedASXL_074196SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30030912 vs. TrEMBL
Match: T1G6Q9 (Dimer_Tnp_hAT domain-containing protein OS=Helobdella robusta OX=6412 GN=20216756 PE=4 SV=1)

HSP 1 Score: 51.6026 bits (122), Expect = 1.866e-9
Identity = 32/59 (54.24%), Postives = 38/59 (64.41%), Query Frame = -3 
Query:  345 NDTVFKRIFNKKEQSEF*IFLSSR-------EIVLLLTFKSSYLYEQGFSAPTETK*KK 500
            ND VFKR+F +KE SEF ++L+S+        I  LL F SSYL EQGFS  TE K KK
Sbjct:   10 NDLVFKRLFTEKELSEFWLYLNSKFPKLSNAAIESLLPFGSSYLCEQGFSTLTEMKSKK 68

HSP 2 Score: 38.5058 bits (88), Expect = 1.866e-9
Identity = 19/37 (51.35%), Postives = 26/37 (70.27%), Query Frame = -2 
Query:  241 KKSVRLQIVDKEMRICL*KLEPCIFLICVDNQA*ISH 351
            KK  RLQ++D+EMR+CL ++ P I LIC   Q+  SH
Sbjct:   67 KKRERLQMIDEEMRVCLSQVHPRIDLICSQKQSQCSH 103
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BLAST of SMED30030912 vs. TrEMBL
Match: T1G894 (Dimer_Tnp_hAT domain-containing protein OS=Helobdella robusta OX=6412 GN=20217291 PE=4 SV=1)

HSP 1 Score: 49.2914 bits (116), Expect = 9.260e-9
Identity = 31/59 (52.54%), Postives = 37/59 (62.71%), Query Frame = -3 
Query:  345 NDTVFKRIFNKKEQSEF*IFLSSR-------EIVLLLTFKSSYLYEQGFSAPTETK*KK 500
            ND VFKR+F ++E SEF + L+S+        I  LL F SSYL EQGFS  TE K KK
Sbjct:   10 NDLVFKRLFTEQELSEFWLCLNSKFPKLSNAAIESLLPFGSSYLCEQGFSTLTEMKSKK 68

HSP 2 Score: 38.5058 bits (88), Expect = 9.260e-9
Identity = 19/37 (51.35%), Postives = 26/37 (70.27%), Query Frame = -2 
Query:  241 KKSVRLQIVDKEMRICL*KLEPCIFLICVDNQA*ISH 351
            KK  RLQ++D+EMR+CL ++ P I LIC   Q+  SH
Sbjct:   67 KKRERLQMIDEEMRVCLSQVHPRIDLICSQKQSQCSH 103
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BLAST of SMED30030912 vs. TrEMBL
Match: T1G0N2 (Dimer_Tnp_hAT domain-containing protein OS=Helobdella robusta OX=6412 GN=20214630 PE=4 SV=1)

HSP 1 Score: 50.447 bits (119), Expect = 7.679e-8
Identity = 32/59 (54.24%), Postives = 37/59 (62.71%), Query Frame = -3 
Query:  345 NDTVFKRIFNKKEQSEF*IFLSSR-------EIVLLLTFKSSYLYEQGFSAPTETK*KK 500
            ND VFKR+F +KE SEF + L+S+        I  LL F SSYL EQGFS  TE K KK
Sbjct:   10 NDLVFKRLFTEKELSEFWLCLNSKFPKLSNAAIESLLPFGSSYLCEQGFSTLTEMKSKK 68

HSP 2 Score: 34.2686 bits (77), Expect = 7.679e-8
Identity = 16/28 (57.14%), Postives = 22/28 (78.57%), Query Frame = -2 
Query:  268 KKSVRLQIVDKEMRICL*KLEPCIFLIC 351
            KK  RLQ++D+EMR+CL ++ P I LIC
Sbjct:   67 KKRERLQMIDEEMRVCLSQVHPRIDLIC 94
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BLAST of SMED30030912 vs. TrEMBL
Match: A0A0P4VJ40 (Putative transposase (Fragment) OS=Rhodnius neglectus OX=72488 PE=2 SV=1)

HSP 1 Score: 41.5874 bits (96), Expect = 2.741e-6
Identity = 20/37 (54.05%), Postives = 26/37 (70.27%), Query Frame = -2 
Query:  241 KKSVRLQIVDKEMRICL*KLEPCIFLICVDNQA*ISH 351
            KK  RLQ++D+EMR+CL KL+P I  IC   Q+  SH
Sbjct:   53 KKRERLQMIDEEMRVCLSKLDPLIDFICSQKQSQCSH 89

HSP 2 Score: 38.1206 bits (87), Expect = 2.741e-6
Identity = 25/54 (46.30%), Postives = 33/54 (61.11%), Query Frame = -3 
Query:  345 KRIFNKKEQSEF*IFL-------SSREIVLLLTFKSSYLYEQGFSAPTETK*KK 485
            +++F +KE SEF + L       S++ +  LL F SSYL EQGFS  TE K KK
Sbjct:    1 RKLFAEKELSEFWLCLNTKFPKLSNKAVESLLPFGSSYLCEQGFSTLTEMKSKK 54
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BLAST of SMED30030912 vs. Planmine SMEST
Match: SMESG000024543.1 (SMESG000024543.1)

HSP 1 Score: 40.817 bits (94), Expect = 5.818e-9
Identity = 27/60 (45.00%), Postives = 35/60 (58.33%), Query Frame = -3 
Query:  342 NDTVFKRIFNKKEQSEF*IFL-------SSREIVLLLTFKSSYLYEQGFSAPTETK*KKA 500
            ND +FKR+ ++ + SEF + L       S++ I  LL F SSYL E GFSA  E K KK 
Sbjct:  292 NDLIFKRMCSEMKLSEFLLSLNNKSFQLSNKAIEPLLPFGSSYLCEHGFSALKEMKSKKP 351

HSP 2 Score: 36.5798 bits (83), Expect = 5.818e-9
Identity = 17/28 (60.71%), Postives = 23/28 (82.14%), Query Frame = -2 
Query:  268 KKSVRLQIVDKEMRICL*KLEPCIFLIC 351
            KK  RL+++D+EMR+CL K+EP I LIC
Sbjct:  349 KKPERLRMIDEEMRVCLSKIEPRINLIC 376
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BLAST of SMED30030912 vs. Planmine SMEST
Match: SMESG000023009.1 (SMESG000023009.1)

HSP 1 Score: 51.2174 bits (121), Expect = 2.776e-8
Identity = 41/97 (42.27%), Postives = 56/97 (57.73%), Query Frame = -3 
Query:  345 KIFQKLDDTEME*IVNHFF------XXXXXXXXXXXXKNDTVFKRIFNKKEQSEF*IFL-------SSREIVLLLTFKSSYLYEQGFSAPTETK*KK 596
            K F  LD +++E I+N F        +  ++     LKND +FKR+F++ E SEF + L       S++ I LLL F+SSYL E GFSA TE K KK
Sbjct:   52 KYFTHLDVSDIEMILNPFMNFNVTNLEEEEEEQLIDLKNDLIFKRMFSEMELSEFWLSLNNKYPQLSNKAIELLLPFRSSYLCEHGFSALTEMKSKK 148
[Close]
BLAST of SMED30030912 vs. Planmine SMEST
Match: SMESG000030482.1 (SMESG000030482.1)

HSP 1 Score: 44.669 bits (104), Expect = 8.553e-6
Identity = 26/54 (48.15%), Postives = 36/54 (66.67%), Query Frame = -2 
Query:  241 FLPL-RARIFGTHRNEVKKSVRLQIVDKEMRICL*KLEPCIFLICVDNQA*ISH 399
             LP  RA IF   ++  KK  RL+++++EMR+CL K+EPCI LIC   Q+  SH
Sbjct:  117 LLPFERAWIFTKMKS--KKRERLRMIEEEMRVCLSKIEPCINLICDTKQSQRSH 168
The following BLAST results are available for this feature:
BLAST of SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
T1G6Q91.866e-954.24Dimer_Tnp_hAT domain-containing protein OS=Helobde... [more]
T1G8949.260e-952.54Dimer_Tnp_hAT domain-containing protein OS=Helobde... [more]
T1G0N27.679e-854.24Dimer_Tnp_hAT domain-containing protein OS=Helobde... [more]
A0A0P4VJ402.741e-654.05Putative transposase (Fragment) OS=Rhodnius neglec... [more]
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BLAST of SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 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 SMED30030912 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000024543.15.818e-945.00SMESG000024543.1[more]
SMESG000023009.12.776e-842.27SMESG000023009.1[more]
SMESG000030482.18.553e-648.15SMESG000030482.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030912 ID=SMED30030912|Name=SMED30030912|organism=Schmidtea mediterranea sexual|type=transcript|length=604bp
TTTATTATGCCGACACTGTTTTAGAAATTTTGTAAATCTTTTTAACATTT
CATTTCTTAAAAAATTTTTATTAATATTCAGAAAATATTTTTCAATCTGA
ATTTATTATTATTTACTAAAACAGTGTCGGGCAACCTTTTTTGCATCGCT
GCACCTCATATAGAAATTCTTAGATTGAAAGGATTTTAACATATGTCATG
ATTATATAGTCTATTACAATTAAACTTTATTTTTGAATGAATGTGAAATT
TAAGCTTGGTTGTCAACACAAATAAGAAAGATACAAGGCTCAAGTTTTCA
AAGACAAATACGCATTTCTTTATCGACAATTTGAAGTCTCACGCTTTTTT
TTACTTCGTTTCTGTGGGTGCCGAAAATCCTTGCTCGTAAAGGTAGGAAC
TTTTAAACGTTAACAGTAGTACTATTTCGCGGCTGCTCAAAAATATTCAG
AACTCTGACTGCTCTTTTTTATTGAAAATCCTTTTGAAAACTGTATCGTT
TTTCAAACATTTTTTTCCACCTTGTTTGCTTCACTTGCCAAAAAAATGGT
TGACTATTCATTCCATTTCAGTATCGTCGAGTTTCTGAAATATTTTGTAA
GATT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell