SMED30014905

Overview
NameSMED30014905
Smed IDSMED30014905
Length (bp)517
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 SMED30014905 (SMED30014905) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014905 (SMED30014905) 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 SMED30014905 (SMED30014905) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014905 (SMED30014905) 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




SMED30014905

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
headSMED30014905SMESG000039178.1 SMESG000036497.1 SMESG000026183.1 SmedASXL_078070SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30014905SMESG000039178.1 SMESG000036497.1 SMESG000026183.1 Contig6886newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30014905 vs. Planmine SMEST
Match: SMESG000079719.1 (SMESG000079719.1)

HSP 1 Score: 144.436 bits (363), Expect = 4.606e-45
Identity = 76/87 (87.36%), Postives = 76/87 (87.36%), Query Frame = 2
Query:  143 MLTAIGSLGFHPVRWGINIDYSV*LPFRFFMDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLPLLARSSDSTGRCCCLLTGIIMAF 403
            MLTAIGSLGF PV WGINIDYSV LPFRFFMDSTSRYKSVFMVRFFR MIRKF Y SIRGIKLPLL R SDSTGRC CLLTGII  F
Sbjct:    1 MLTAIGSLGFRPVCWGINIDYSVELPFRFFMDSTSRYKSVFMVRFFREMIRKFYYSSIRGIKLPLLTRFSDSTGRCRCLLTGIINGF 87          

HSP 2 Score: 49.6766 bits (117), Expect = 2.913e-8
Identity = 22/23 (95.65%), Postives = 22/23 (95.65%), Query Frame = 1
Query:  394 NGFHPSSLWIFDHTNGKVLVYFL 462
            NGFHP SLWIFDHTNGKVLVYFL
Sbjct:   85 NGFHPPSLWIFDHTNGKVLVYFL 107          
BLAST of SMED30014905 vs. Planmine SMEST
Match: SMESG000039178.1 (SMESG000039178.1)

HSP 1 Score: 105.531 bits (262), Expect = 2.702e-32
Identity = 53/57 (92.98%), Postives = 53/57 (92.98%), Query Frame = 2
Query:  233 MDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLPLLARSSDSTGRCCCLLTGIIMAF 403
            MDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLPLLAR SDSTGRC CLLTGII  F
Sbjct:    1 MDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLPLLARPSDSTGRCRCLLTGIINGF 57          

HSP 2 Score: 50.8322 bits (120), Expect = 2.702e-32
Identity = 22/23 (95.65%), Postives = 22/23 (95.65%), Query Frame = 1
Query:  394 NGFHPSSLWIFDHTNGKVLVYFL 462
            NGFHPS LWIFDHTNGKVLVYFL
Sbjct:   55 NGFHPSRLWIFDHTNGKVLVYFL 77          
BLAST of SMED30014905 vs. Planmine SMEST
Match: SMESG000036497.1 (SMESG000036497.1)

HSP 1 Score: 99.7525 bits (247), Expect = 1.358e-28
Identity = 50/57 (87.72%), Postives = 51/57 (89.47%), Query Frame = 2
Query:  233 MDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLPLLARSSDSTGRCCCLLTGIIMAF 403
            MDSTSRYKSVFMVRFF GMIRKFNYLS+R IKLPLLAR SDSTGRC CLLTGII  F
Sbjct:    1 MDSTSRYKSVFMVRFFPGMIRKFNYLSLRSIKLPLLARPSDSTGRCGCLLTGIINGF 57          

HSP 2 Score: 43.8986 bits (102), Expect = 1.358e-28
Identity = 18/22 (81.82%), Postives = 20/22 (90.91%), Query Frame = 1
Query:  394 NGFHPSSLWIFDHTNGKVLVYF 459
            NGFHPSSLWIFDHTNGK+  +F
Sbjct:   55 NGFHPSSLWIFDHTNGKISSFF 76          
BLAST of SMED30014905 vs. Planmine SMEST
Match: SMESG000039178.1 (SMESG000039178.1)

HSP 1 Score: 91.2781 bits (225), Expect = 5.050e-28
Identity = 46/50 (92.00%), Postives = 46/50 (92.00%), Query Frame = 2
Query:  254 KSVFMVRFFRGMIRKFNYLSIRGIKLPLLARSSDSTGRCCCLLTGIIMAF 403
            KSVFMVRFFRGMIRKFNYLSIRGIKLPLLAR SDSTGRC CLLTGII  F
Sbjct:    3 KSVFMVRFFRGMIRKFNYLSIRGIKLPLLARPSDSTGRCRCLLTGIINGF 52          

HSP 2 Score: 50.447 bits (119), Expect = 5.050e-28
Identity = 22/23 (95.65%), Postives = 22/23 (95.65%), Query Frame = 1
Query:  394 NGFHPSSLWIFDHTNGKVLVYFL 462
            NGFHPS LWIFDHTNGKVLVYFL
Sbjct:   50 NGFHPSRLWIFDHTNGKVLVYFL 72          
BLAST of SMED30014905 vs. Planmine SMEST
Match: SMESG000079728.1 (SMESG000079728.1)

HSP 1 Score: 65.855 bits (159), Expect = 2.290e-17
Identity = 30/36 (83.33%), Postives = 31/36 (86.11%), Query Frame = 2
Query:  227 FFMDSTSRYKSVFMVRFFRGMIRKFNYLSIRGIKLP 334
            F MDS SRYKSVFMVRFFR MIRKFNY SIRG+ LP
Sbjct:  479 FAMDSISRYKSVFMVRFFREMIRKFNYSSIRGVMLP 514          

HSP 2 Score: 40.0466 bits (92), Expect = 2.290e-17
Identity = 16/20 (80.00%), Postives = 17/20 (85.00%), Query Frame = 1
Query:  334 PASSILRFNRTMLLPPDWNY 393
            PA+S LRFNR M LPPDWNY
Sbjct:  515 PANSTLRFNRMMPLPPDWNY 534          
The following BLAST results are available for this feature:
BLAST of SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 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 SMED30014905 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079719.14.606e-4587.36SMESG000079719.1[more]
SMESG000039178.12.702e-3292.98SMESG000039178.1[more]
SMESG000036497.11.358e-2887.72SMESG000036497.1[more]
SMESG000039178.15.050e-2892.00SMESG000039178.1[more]
SMESG000079728.12.290e-1783.33SMESG000079728.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014905 ID=SMED30014905|Name=SMED30014905|organism=Schmidtea mediterranea sexual|type=transcript|length=517bp
CTATACTAAATTTTATGCATAATTGGTTGCTTAGTAACCTTAAATGGCGA
CGGTCAAATCTTCAACGTAACGTTCTTTAATTATGGAATGAAGGAGAAGA
AAACTAAATAAAAAAAATGAGATGTCGCGTGTGAAAAACGGCATGCTAAC
TGCAATCGGCTCGTTGGGTTTCCACCCTGTGCGTTGGGGAATTAATATTG
ATTATTCTGTATAGTTGCCTTTCAGATTTTTCATGGATTCCACATCCAGA
TATAAGTCGGTGTTTATGGTCAGGTTTTTCCGGGGAATGATTAGAAAGTT
CAATTATTTGTCTATAAGAGGCATAAAGCTTCCCCTGCTAGCTCGATCCT
CAGATTCAACCGGACGATGCTGTTGCCTCCTGACTGGAATTATAATGGCT
TTCACCCATCTAGTTTATGGATCTTTGATCATACCAATGGGAAGGTTTTA
GTGTATTTCTTGTGATGACTTCTCTAGGTAGTACTCGTTAGTTGTGATTA
TGATAAATCGATTGGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0002089reproductive organ