SMED30005089

Overview
NameSMED30005089
Smed IDSMED30005089
Length (bp)807
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 SMED30005089 (SMED30005089) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005089 (SMED30005089) 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 SMED30005089 (SMED30005089) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005089 (SMED30005089) 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




SMED30005089

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
parenchymal cellSMED30005089 dd_Smed_v4_13407_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30005089 vs. Planmine SMEST
Match: SMESG000015004.1 (SMESG000015004.1)

HSP 1 Score: 69.3218 bits (168), Expect = 8.566e-15
Identity = 35/46 (76.09%), Postives = 39/46 (84.78%), Query Frame = 3
Query:  384 EARQRAEFSLYEF*EQERKALLKVVMARRRLRRVNAAIAAGEIPNT 521
            EARQRAEFSLY + +QERKA  KV MARRRL+ VNAAI AGEIP+T
Sbjct:   35 EARQRAEFSLYGYEDQERKAHCKVFMARRRLKNVNAAIVAGEIPST 80          
BLAST of SMED30005089 vs. Planmine SMEST
Match: SMESG000025570.1 (SMESG000025570.1)

HSP 1 Score: 67.3958 bits (163), Expect = 8.848e-14
Identity = 38/75 (50.67%), Postives = 48/75 (64.00%), Query Frame = 1
Query:  511 YPTPEYGVSLKLDDPALDQMHT-TSVVLPVRMFRGPVQDRKTTGRRR--SCLKQS*PTNERTKASTRI*IQKRFP 726
            +  PEYGVS +LDDPAL++MH  TSVVLPVRMFR  V++R    R++  +      P  + T AST    QKRFP
Sbjct:   52 WYAPEYGVSFELDDPALEKMHAPTSVVLPVRMFRETVRNRIGNQRKKGDNAYNGRHPPTDVTYASTSTEWQKRFP 126          
BLAST of SMED30005089 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 46.9802 bits (110), Expect = 1.191e-11
Identity = 25/46 (54.35%), Postives = 33/46 (71.74%), Query Frame = 3
Query:  384 EARQRAEFSLYEF*EQERKALLKVVMARRRLRRVNAAIAAGEIPNT 521
            EARQRAEFS  +  + E+K   K V+AR+RL +VN  IA+G IP+T
Sbjct:  733 EARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPST 778          

HSP 2 Score: 40.817 bits (94), Expect = 1.191e-11
Identity = 19/37 (51.35%), Postives = 26/37 (70.27%), Query Frame = 1
Query:  520 PEYGVSLKLDDPALDQMHT-TSVVLPVRMFRGPVQDR 627
            PEYGVS +LDDP L QM   T +VLP R+ +  +++R
Sbjct:  783 PEYGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNR 819          
BLAST of SMED30005089 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1)

HSP 1 Score: 46.9802 bits (110), Expect = 1.200e-11
Identity = 25/46 (54.35%), Postives = 33/46 (71.74%), Query Frame = 3
Query:  384 EARQRAEFSLYEF*EQERKALLKVVMARRRLRRVNAAIAAGEIPNT 521
            EARQRAEFS  +  + E+K   K V+AR+RL +VN  IA+G IP+T
Sbjct:  734 EARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPST 779          

HSP 2 Score: 40.817 bits (94), Expect = 1.200e-11
Identity = 19/37 (51.35%), Postives = 26/37 (70.27%), Query Frame = 1
Query:  520 PEYGVSLKLDDPALDQMHT-TSVVLPVRMFRGPVQDR 627
            PEYGVS +LDDP L QM   T +VLP R+ +  +++R
Sbjct:  784 PEYGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNR 820          
BLAST of SMED30005089 vs. Planmine SMEST
Match: SMESG000052862.1 (SMESG000052862.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.664e-11
Identity = 26/46 (56.52%), Postives = 33/46 (71.74%), Query Frame = 3
Query:  384 EARQRAEFSLYEF*EQERKALLKVVMARRRLRRVNAAIAAGEIPNT 521
            EARQRAEF+  +  E ERK   K V+AR+RL +VN  IA+G IP+T
Sbjct: 2329 EARQRAEFTAMKMEELERKYQRKAVLARQRLVQVNRDIASGAIPST 2374          

HSP 2 Score: 36.5798 bits (83), Expect = 1.664e-11
Identity = 18/37 (48.65%), Postives = 26/37 (70.27%), Query Frame = 1
Query:  520 PEYGVSLKLDDPALDQMHT-TSVVLPVRMFRGPVQDR 627
            PEYGVS +LDDP L QM T T +VL  ++ +  +++R
Sbjct: 2379 PEYGVSFELDDPRLKQMTTPTKLVLLEKLIQSTLRNR 2415          
The following BLAST results are available for this feature:
BLAST of SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 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 SMED30005089 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000015004.18.566e-1576.09SMESG000015004.1[more]
SMESG000025570.18.848e-1450.67SMESG000025570.1[more]
SMESG000035366.11.191e-1154.35SMESG000035366.1[more]
SMESG000035366.11.200e-1154.35SMESG000035366.1[more]
SMESG000052862.11.664e-1156.52SMESG000052862.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005089 ID=SMED30005089|Name=SMED30005089|organism=Schmidtea mediterranea sexual|type=transcript|length=807bp
TAATCATAAATAATTAAGGGAGAAGAAATAATTAAACATCCGGTCCGATT
TAAGTACCAATAAGAATTCCATTATATGCATGAGAAAATGACTCATCCAC
ACTTGTGGAGACTATTTTTCCAAAATTTAATCACCATTTATTCATTTAAA
TTATACTACCAATAATCAACCCAATGAGCGATAATGGATCAACCGCTAAA
GGAAGTGCCTGCGCCAAGGAGCAATCTGACGTAGAGTATAAGAAACCACG
AGCATGGGAAATGAATCGGATCTCCAACAATGAGGGACAGTTTGCACCAG
TTGAGTCGGACTATCGAGGGAGTAGTACATGGAGTGACAATAACCGAGTC
ATTGTGAAGTTTCCGTATCTTCTATTCTGCTACGAGGCGCGCCAACGAGC
GGAATTCTCTCTGTATGAATTTTAAGAACAAGAAAGGAAAGCTCTCTTGA
AAGTTGTCATGGCTCGGAGAAGATTAAGACGAGTCAATGCAGCTATTGCG
GCTGGAGAAATACCCAACACCTGAATATGGCGTGTCTCTCAAATTGGACG
ACCCAGCGTTAGATCAAATGCATACCACCAGCGTGGTGTTGCCAGTGAGG
ATGTTTCGTGGACCAGTCCAGGATCGGAAGACAACAGGAAGAAGGCGATC
ATGCCTAAAACAGTCCTAACCCACCAACGAACGGACAAAAGCATCAACTA
GAATTTAGATACAGAAAAGATTCCCATAACTGAATGTGAAAATAGAACGA
AAACGAAAAGTTTCGTTGGACTAGAATAAATCTTATGTTGTTGCATTGTC
ATTATTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell