SMED30020094

Overview
NameSMED30020094
Smed IDSMED30020094
Length (bp)568
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 SMED30020094 (SMED30020094) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020094 (SMED30020094) 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



SMED30020094

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
X2 cellSMED30020094 SmedASXL_019287SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020094 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010965:10607..11418 +2762
Homology
[Close]
BLAST of SMED30020094 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 73.559 bits (179), Expect = 3.043e-23
Identity = 35/92 (38.04%), Postives = 57/92 (61.96%), Query Frame = 2 
Query:  152 SGSKKEEYHDLADRNTYTQDRVEARRANEMSWRNDSRITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVIKQEPG 427
            +G KK+    +++ N  +   +  RR    SW ++SR+T+++P   AAR    LW+ GY +ST G + W  RS S+ +E++LPS+VI +EPG
Sbjct: 2073 NGLKKDNECQISNINVISPKEIN-RRDPYGSWNDNSRVTLQIPSASAARYRQMLWDNGYLLSTYGDSSWPRRSESQAEEIELPSIVINREPG 2163

HSP 2 Score: 52.373 bits (124), Expect = 3.043e-23
Identity = 26/50 (52.00%), Postives = 35/50 (70.00%), Query Frame = 3 
Query:  417 RNPAKEARQQVEFSLTR*QALERKFRWKVQLARSYLA*VNADIAAGRITS 566
            +NPA+EARQ+ EF+  + + LERK++ K  LAR  L  VN DIA+G I S
Sbjct: 2164 KNPAREARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPS 2213
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BLAST of SMED30020094 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1)

HSP 1 Score: 77.0258 bits (188), Expect = 3.893e-23
Identity = 35/82 (42.68%), Postives = 51/82 (62.20%), Query Frame = 2 
Query:  182 LADRNTYTQDRVEARRANEMSWRNDSRITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVIKQEPG 427
            + D N  TQ   E RR    SW ++SR+T+++P   AAR    LW+ GY +ST G + W  RS  + +E++LPS+ IK+EPG
Sbjct: 1310 MKDLNAITQKEFEYRRDTSGSWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPG 1391

HSP 2 Score: 48.521 bits (114), Expect = 3.893e-23
Identity = 25/49 (51.02%), Postives = 33/49 (67.35%), Query Frame = 3 
Query:  420 NPAKEARQQVEFSLTR*QALERKFRWKVQLARSYLA*VNADIAAGRITS 566
            NPA+EA Q+ E++  + + LERK+  K  LAR  LA VN DIA+G I S
Sbjct: 1393 NPAREAHQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPS 1441
[Close]
BLAST of SMED30020094 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 72.0182 bits (175), Expect = 6.475e-23
Identity = 31/68 (45.59%), Postives = 46/68 (67.65%), Query Frame = 2 
Query:  224 RRANEMSWRNDSRITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVIKQEPG 427
            RR    SW ++SR+T+++P   AAR    LW+ GY +ST G + W  RS S+ +E++LPS+VI +EPG
Sbjct: 2261 RRDPYGSWNDNSRVTLQIPSASAARYRQMLWDNGYLLSTYGDSSWPRRSESQAEEIELPSIVINREPG 2328

HSP 2 Score: 52.7582 bits (125), Expect = 6.475e-23
Identity = 26/50 (52.00%), Postives = 35/50 (70.00%), Query Frame = 3 
Query:  417 RNPAKEARQQVEFSLTR*QALERKFRWKVQLARSYLA*VNADIAAGRITS 566
            +NPA+EARQ+ EF+  + + LERK++ K  LAR  L  VN DIA+G I S
Sbjct: 2329 KNPAREARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPS 2378
[Close]
BLAST of SMED30020094 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 72.0182 bits (175), Expect = 7.323e-23
Identity = 31/68 (45.59%), Postives = 46/68 (67.65%), Query Frame = 2 
Query:  224 RRANEMSWRNDSRITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVIKQEPG 427
            RR    SW ++SR+T+++P   AAR    LW+ GY +ST G + W  RS S+ +E++LPS+VI +EPG
Sbjct: 2256 RRDPYGSWNDNSRVTLQIPSASAARYRQMLWDNGYLLSTYGDSSWPRRSESQAEEIELPSIVINREPG 2323

HSP 2 Score: 52.373 bits (124), Expect = 7.323e-23
Identity = 26/50 (52.00%), Postives = 35/50 (70.00%), Query Frame = 3 
Query:  417 RNPAKEARQQVEFSLTR*QALERKFRWKVQLARSYLA*VNADIAAGRITS 566
            +NPA+EARQ+ EF+  + + LERK++ K  LAR  L  VN DIA+G I S
Sbjct: 2324 KNPAREARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPS 2373
[Close]
BLAST of SMED30020094 vs. Planmine SMEST
Match: SMESG000014849.1 (SMESG000014849.1)

HSP 1 Score: 71.633 bits (174), Expect = 9.595e-23
Identity = 30/68 (44.12%), Postives = 45/68 (66.18%), Query Frame = 2 
Query:  224 RRANEMSWRNDSRITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVIKQEPG 427
            RR    +W ++SR+T+++P   AAR    LW+ GY +ST G + W  RS  R +E++LPS+ IK+EPG
Sbjct:  876 RRDPHGNWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYRAEEIELPSIAIKREPG 943

HSP 2 Score: 52.373 bits (124), Expect = 9.595e-23
Identity = 26/49 (53.06%), Postives = 34/49 (69.39%), Query Frame = 3 
Query:  420 NPAKEARQQVEFSLTR*QALERKFRWKVQLARSYLA*VNADIAAGRITS 566
            NPA+EARQ+ E++  + + LERK+  K  LAR  LA VN DIA+G I S
Sbjct:  945 NPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGVIPS 993
The following BLAST results are available for this feature:
BLAST of SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 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 SMED30020094 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000052862.13.043e-2338.04SMESG000052862.1[more]
SMESG000042475.13.893e-2342.68SMESG000042475.1[more]
SMESG000052862.16.475e-2345.59SMESG000052862.1[more]
SMESG000052862.17.323e-2345.59SMESG000052862.1[more]
SMESG000014849.19.595e-2344.12SMESG000014849.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020094 ID=SMED30020094|Name=SMED30020094|organism=Schmidtea mediterranea sexual|type=transcript|length=568bp
ACTAATTGTAATTAGCTCGCTGCTATAAATACCGATGAAGAAGAACACCT
AATAAATGATGAAACGATCAAACAGAATTGAAATTGGCTAATCATCTGAA
CCCCGTTAATAGATGACCCAGCTGAACAATCAGGATATCCGACCGATCGA
ATCAGGAAGCAAAAAGGAGGAGTATCACGACTTGGCAGACAGGAATACTT
ATACACAGGATCGGGTAGAAGCCAGGCGAGCCAATGAAATGTCGTGGAGA
AATGATTCAAGGATCACTGTGAAATTACCAGGAAAGATGGCTGCTCGATG
TAGTCACGCATTATGGGAAATGGGCTACACCGTATCAACTGCCGGAGGAA
ACGAATGGCATATTCGTTCAGGATCGCGGAACGATGAAGTGGATCTGCCC
AGCGTGGTAATCAAGCAGGAACCCGGCTAAGGAGGCTCGTCAGCAAGTCG
AATTTTCGTTGACGCGTTAACAGGCGTTGGAACGAAAATTTCGATGGAAG
GTACAGCTGGCAAGAAGTTATTTGGCTTGAGTTAACGCTGATATTGCGGC
GGGACGAATAACAAGCAC
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protein sequence of SMED30020094-orf-1

>SMED30020094-orf-1 ID=SMED30020094-orf-1|Name=SMED30020094-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
MTQLNNQDIRPIESGSKKEEYHDLADRNTYTQDRVEARRANEMSWRNDSR
ITVKLPGKMAARCSHALWEMGYTVSTAGGNEWHIRSGSRNDEVDLPSVVI
KQEPG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell