SMED30031494

Overview
NameSMED30031494
Smed IDSMED30031494
Length (bp)426
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 SMED30031494 (SMED30031494) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031494 (SMED30031494) 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 SMED30031494 (SMED30031494) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031494 (SMED30031494) 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




SMED30031494

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 cellSMED30031494 dd_Smed_v4_23616_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
Alignments
SMED30031494 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000021:247739..248572 +2018
v31.003720:25574..25987 +1333
Homology
BLAST of SMED30031494 vs. Planmine SMEST
Match: SMESG000053804.1 (SMESG000053804.1)

HSP 1 Score: 68.9366 bits (167), Expect = 7.394e-24
Identity = 33/50 (66.00%), Postives = 39/50 (78.00%), Query Frame = -3
Query:  212 MNAIKEISHELRKLRRENTYLHQQCIQLSRELQRTKAPWVEPSRMKKFYQ 361
            M+AI+ I  EL+KLRREN  LHQQC+QLSRELQ  KA W EPSR+K  Y+
Sbjct:    1 MDAIQGIGVELKKLRRENDCLHQQCLQLSRELQWIKATWSEPSRVKLLYE 50          

HSP 2 Score: 52.373 bits (124), Expect = 7.394e-24
Identity = 24/36 (66.67%), Postives = 29/36 (80.56%), Query Frame = -2
Query:  105 KANGAQKGWQEEKTLNQAQRVQIRELEVVVEASQEG 212
            K + AQKGWQ+E+TLNQ QR+QIR L+V V A QEG
Sbjct:   51 KNDAAQKGWQDERTLNQTQRIQIRGLKVAVAADQEG 86          

HSP 3 Score: 25.7942 bits (55), Expect = 7.394e-24
Identity = 10/14 (71.43%), Postives = 10/14 (71.43%), Query Frame = -1
Query:   67 GSAVTYPLVFAPTQ 108
            G AV Y LVFAP Q
Sbjct:   86 GRAVMYHLVFAPAQ 99          
BLAST of SMED30031494 vs. Planmine SMEST
Match: SMESG000057359.1 (SMESG000057359.1)

HSP 1 Score: 72.0182 bits (175), Expect = 2.220e-23
Identity = 35/61 (57.38%), Postives = 42/61 (68.85%), Query Frame = -3
Query:  212 PIMLEKITFKAMNAIKEISHELRKLRRENTYLHQQCIQLSRELQRTKAPWVEPSRMKKFYQ 394
            PI++  I   AMN IK I  EL+KLR EN  LHQQC+QLS E QR    W+EPSR+K+ YQ
Sbjct:    3 PILIMLIN-SAMNTIKNIGRELKKLRTENANLHQQCVQLSCEQQRINDTWIEPSRVKRLYQ 62          

HSP 2 Score: 53.5286 bits (127), Expect = 2.220e-23
Identity = 27/47 (57.45%), Postives = 31/47 (65.96%), Query Frame = -2
Query:   72 KANGAQKGWQEEKTLNQAQRVQIRELEVVVEASQEGVRSLTPWCLHP 212
            K + AQKG QEEK LNQAQ++QIR LE+ V ASQEG     P    P
Sbjct:   63 KISAAQKGLQEEKALNQAQKIQIRGLEIAVAASQEGSAVTYPLVFAP 109          
BLAST of SMED30031494 vs. Planmine SMEST
Match: SMESG000035021.1 (SMESG000035021.1)

HSP 1 Score: 67.781 bits (164), Expect = 5.253e-23
Identity = 29/50 (58.00%), Postives = 41/50 (82.00%), Query Frame = -3
Query:  212 MNAIKEISHELRKLRRENTYLHQQCIQLSRELQRTKAPWVEPSRMKKFYQ 361
            M+A+++IS E +  R+ENT LHQQC+QLSREL+R +A W EP+R+K+ YQ
Sbjct:  401 MDAMQKISKEFKDRRKENTNLHQQCLQLSRELKRIRATWSEPARVKRLYQ 450          

HSP 2 Score: 51.9878 bits (123), Expect = 5.253e-23
Identity = 24/34 (70.59%), Postives = 29/34 (85.29%), Query Frame = -2
Query:  105 NGAQKGWQEEKTLNQAQRVQIRELEVVVEASQEG 206
            + AQKGWQE++ LNQAQ+VQIR +EV V ASQEG
Sbjct:  453 DAAQKGWQEKRALNQAQKVQIRVMEVAVAASQEG 486          

HSP 3 Score: 24.6386 bits (52), Expect = 5.253e-23
Identity = 10/14 (71.43%), Postives = 10/14 (71.43%), Query Frame = -1
Query:   67 GSAVTYPLVFAPTQ 108
            G AVTYPL FA  Q
Sbjct:  486 GHAVTYPLAFASAQ 499          
BLAST of SMED30031494 vs. Planmine SMEST
Match: SMESG000021767.1 (SMESG000021767.1)

HSP 1 Score: 68.9366 bits (167), Expect = 6.001e-23
Identity = 30/50 (60.00%), Postives = 43/50 (86.00%), Query Frame = -3
Query:  212 MNAIKEISHELRKLRRENTYLHQQCIQLSRELQRTKAPWVEPSRMKKFYQ 361
            M+A+++IS++L+ LR+E T LHQQC+QLSRELQR +A W EP+R+K+ YQ
Sbjct:   63 MDAMQKISNKLKNLRKEITNLHQQCLQLSRELQRIRATWSEPARVKRLYQ 112          

HSP 2 Score: 55.0694 bits (131), Expect = 6.001e-23
Identity = 28/47 (59.57%), Postives = 31/47 (65.96%), Query Frame = -2
Query:   72 KANGAQKGWQEEKTLNQAQRVQIRELEVVVEASQEGVRSLTPWCLHP 212
            K +  QKGWQEE+ LNQAQ+VQIR LEV V ASQEG     P    P
Sbjct:  113 KIDAVQKGWQEERFLNQAQKVQIRGLEVAVAASQEGQAVTYPMVFVP 159          
BLAST of SMED30031494 vs. Planmine SMEST
Match: SMESG000077887.1 (SMESG000077887.1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.925e-21
Identity = 30/50 (60.00%), Postives = 41/50 (82.00%), Query Frame = -3
Query:  212 MNAIKEISHELRKLRRENTYLHQQCIQLSRELQRTKAPWVEPSRMKKFYQ 361
            M+A+++I  EL+ LR+EN  LHQQC+QLSRELQR KA W +P+R+K+ YQ
Sbjct:    1 MDAMQKIGKELKDLRKENANLHQQCLQLSRELQRIKATWSDPTRVKRLYQ 50          

HSP 2 Score: 40.0466 bits (92), Expect = 1.925e-21
Identity = 21/35 (60.00%), Postives = 25/35 (71.43%), Query Frame = -2
Query:  108 KANGAQKGWQEEKTLNQAQRVQIRELEVVVEASQE 212
            K + AQKG +EE+  NQAQ VQIR LE+ V A QE
Sbjct:   51 KIDTAQKGCREERVQNQAQNVQIRGLEIAVAAGQE 85          

HSP 3 Score: 27.7202 bits (60), Expect = 1.925e-21
Identity = 15/34 (44.12%), Postives = 17/34 (50.00%), Query Frame = -1
Query:   46 SAVTYPLVFAPTQ--------------PVSRRNI 105
             AVTYPLVFAP Q              P SR+N+
Sbjct:   87 QAVTYPLVFAPAQVAYKHAMSTENQPFPTSRKNL 120          
The following BLAST results are available for this feature:
BLAST of SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 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 SMED30031494 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000053804.17.394e-2466.00SMESG000053804.1[more]
SMESG000057359.12.220e-2357.38SMESG000057359.1[more]
SMESG000035021.15.253e-2358.00SMESG000035021.1[more]
SMESG000021767.16.001e-2360.00SMESG000021767.1[more]
SMESG000077887.11.925e-2160.00SMESG000077887.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031494 ID=SMED30031494|Name=SMED30031494|organism=Schmidtea mediterranea sexual|type=transcript|length=426bp
GGTTCTGGCGCTTTCTACGCTCTCGTTCGGCCTTTATGGGCCTCGTATGT
TTCTTCGACTCACTGGTTGCGTGGGTGCAAACACCAAGGGGTAAGTGACC
GCACTCCCTCTTGGCTGGCCTCGACGACAACTTCCAGCTCGCGAATTTGG
ACTCTTTGGGCCTGGTTCAAGGTCTTCTCTTCCTGCCAACCCTTCTGAGC
CCCGTTAGCCTTTGGTAGAACTTCTTCATCCGTGAAGGCTCTACCCACGG
TGCTTTCGTCCGTTGTAGCTCTCGGCTGAGCTGAATACACTGCTGGTGGA
GATAAGTGTTCTCCCTCCTTAACTTCCTCAGTTCGTGGCTGATTTCTTTT
ATGGCGTTCATAGCCTTGAACGTGATCTTCTCGAGCATAATAGGGTTCCA
CTTTCTCCATGCGGCCGACTTCGTAG
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protein sequence of SMED30031494-orf-1

>SMED30031494-orf-1 ID=SMED30031494-orf-1|Name=SMED30031494-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=122bp
YEVGRMEKVEPYYAREDHVQGYERHKRNQPRTEEVKEGEHLSPPAVYSAQ
PRATTDESTVGRAFTDEEVLPKANGAQKGWQEEKTLNQAQRVQIRELEVV
VEASQEGVRSLTPWCLHPRNQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell