SMED30011371

Overview
NameSMED30011371
Smed IDSMED30011371
Length (bp)881
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 SMED30011371 (SMED30011371) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011371 (SMED30011371) 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 SMED30011371 (SMED30011371) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30011371 (SMED30011371) 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



SMED30011371

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 cellSMED30011371 SmedASXL_057132SmedAsxl_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
SMED30011371 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000043:78871..79751 -4405
Homology
[Close]
BLAST of SMED30011371 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1)

HSP 1 Score: 131.339 bits (329), Expect = 1.935e-46
Identity = 63/110 (57.27%), Postives = 79/110 (71.82%), Query Frame = -2 
Query:  110 GQEPAREARQRAE-ISLYCLDSQKTFHWRANLARRHLARVNADIVSRLIPSTDGFAPEYEVSFDRDDPRLMNMEGPTKLILPDWLVQPALLDRLGQRQNGDHMYARRFLQ 436
            G  PAREARQRAE +++   + ++ +H +A LAR+ LA+VN DI S  IPSTDGF PEY VSF+ DDPRLM M  PTK+++P+ LVQ  L +RLG RQ GDH YA R  Q
Sbjct: 1196 GHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQ 1305

HSP 2 Score: 73.1738 bits (178), Expect = 1.935e-46
Identity = 33/64 (51.56%), Postives = 50/64 (78.12%), Query Frame = -3 
Query:  427 DWTDGSRITLQVPAQSAARHRQSL*NHGYSLATYGENR*QCRPEDRNDEVDLPSVAIKKELGRN 618
            +W+D SR+TLQ+P+ SAAR+RQ L ++GY L+TYG++    R E + +E++LPS+AIK+E G N
Sbjct: 1135 NWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHN 1198
[Close]
BLAST of SMED30011371 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 129.413 bits (324), Expect = 2.361e-45
Identity = 63/110 (57.27%), Postives = 79/110 (71.82%), Query Frame = -2 
Query:  110 GQEPAREARQRAE-ISLYCLDSQKTFHWRANLARRHLARVNADIVSRLIPSTDGFAPEYEVSFDRDDPRLMNMEGPTKLILPDWLVQPALLDRLGQRQNGDHMYARRFLQ 436
            G  PAREARQRAE +++   + ++ +H +A LAR+ LA+VN DI S  IPSTDGF PEY VSF+ DDPRLM M  PTK+++P+ LVQ  L +RLG RQ GDH YA R  Q
Sbjct:  834 GHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQ 943

HSP 2 Score: 72.0182 bits (175), Expect = 2.361e-45
Identity = 33/64 (51.56%), Postives = 50/64 (78.12%), Query Frame = -3 
Query:  427 DWTDGSRITLQVPAQSAARHRQSL*NHGYSLATYGENR*QCRPEDRNDEVDLPSVAIKKELGRN 618
            +W+D SR+TLQ+P+ SAAR+RQ L ++GY L+TYG++    R E + +E++LPS+AIK+E G N
Sbjct:  773 NWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHN 836
[Close]
BLAST of SMED30011371 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1)

HSP 1 Score: 128.257 bits (321), Expect = 5.586e-45
Identity = 63/110 (57.27%), Postives = 79/110 (71.82%), Query Frame = -2 
Query:  110 GQEPAREARQRAE-ISLYCLDSQKTFHWRANLARRHLARVNADIVSRLIPSTDGFAPEYEVSFDRDDPRLMNMEGPTKLILPDWLVQPALLDRLGQRQNGDHMYARRFLQ 436
            G  PAREARQRAE +++   + ++ +H +A LAR+ LA+VN DI S  IPSTDGF PEY VSF+ DDPRLM M  PTK+++P+ LVQ  L +RLG RQ GDH YA R  Q
Sbjct:  760 GHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQ 869

HSP 2 Score: 71.633 bits (174), Expect = 5.586e-45
Identity = 33/64 (51.56%), Postives = 50/64 (78.12%), Query Frame = -3 
Query:  427 DWTDGSRITLQVPAQSAARHRQSL*NHGYSLATYGENR*QCRPEDRNDEVDLPSVAIKKELGRN 618
            +W+D SR+TLQ+P+ SAAR+RQ L ++GY L+TYG++    R E + +E++LPS+AIK+E G N
Sbjct:  699 NWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHN 762
[Close]
BLAST of SMED30011371 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 118.627 bits (296), Expect = 1.459e-44
Identity = 57/107 (53.27%), Postives = 76/107 (71.03%), Query Frame = -2 
Query:  119 GQEPAREARQRAE-ISLYCLDSQKTFHWRANLARRHLARVNADIVSRLIPSTDGFAPEYEVSFDRDDPRLMNMEGPTKLILPDWLVQPALLDRLGQRQNGDHMYARR 436
            G+ PARE  QRAE  S+   + ++ +H +A LAR+ LA++N DI S +IPSTD F P Y VSF+ DDPRL+ M  PTKL++P+ L+QP L +RLG R+ GDH YA R
Sbjct:  730 GRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQPGLRNRLGSRRTGDHTYASR 836

HSP 2 Score: 79.7221 bits (195), Expect = 1.459e-44
Identity = 38/63 (60.32%), Postives = 51/63 (80.95%), Query Frame = -3 
Query:  427 WTDGSRITLQVPAQSAARHRQSL*NHGYSLATYGENR*QCRPEDRNDEVDLPSVAIKKELGRN 615
            W D S+ITLQ+   SAAR+RQ+L ++GY+L+TYGE+    RP+DR DEV+LPS+AIK+E GRN
Sbjct:  670 WRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRN 732
[Close]
BLAST of SMED30011371 vs. Planmine SMEST
Match: SMESG000046313.1 (SMESG000046313.1)

HSP 1 Score: 118.627 bits (296), Expect = 1.708e-44
Identity = 57/107 (53.27%), Postives = 76/107 (71.03%), Query Frame = -2 
Query:  119 GQEPAREARQRAE-ISLYCLDSQKTFHWRANLARRHLARVNADIVSRLIPSTDGFAPEYEVSFDRDDPRLMNMEGPTKLILPDWLVQPALLDRLGQRQNGDHMYARR 436
            G+ PARE  QRAE  S+   + ++ +H +A LAR+ LA++N DI S +IPSTD F P Y VSF+ DDPRL+ M  PTKL++P+ L+QP L +RLG R+ GDH YA R
Sbjct:  678 GRNPAREVHQRAEYTSMKMEEMERKYHRKAVLARQRLAQINRDIASGVIPSTDSFPPTYGVSFELDDPRLLQMTAPTKLVIPEELIQPGLRNRLGSRRTGDHTYASR 784

HSP 2 Score: 79.7221 bits (195), Expect = 1.708e-44
Identity = 38/63 (60.32%), Postives = 51/63 (80.95%), Query Frame = -3 
Query:  427 WTDGSRITLQVPAQSAARHRQSL*NHGYSLATYGENR*QCRPEDRNDEVDLPSVAIKKELGRN 615
            W D S+ITLQ+   SAAR+RQ+L ++GY+L+TYGE+    RP+DR DEV+LPS+AIK+E GRN
Sbjct:  618 WRDDSQITLQISNASAARYRQALWDNGYTLSTYGESSWPRRPKDREDEVELPSIAIKREPGRN 680
The following BLAST results are available for this feature:
BLAST of SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 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 SMED30011371 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044971.11.935e-4657.27SMESG000044971.1[more]
SMESG000031842.12.361e-4557.27SMESG000031842.1[more]
SMESG000031842.15.586e-4557.27SMESG000031842.1[more]
SMESG000046313.11.459e-4453.27SMESG000046313.1[more]
SMESG000046313.11.708e-4453.27SMESG000046313.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011371 ID=SMED30011371|Name=SMED30011371|organism=Schmidtea mediterranea sexual|type=transcript|length=881bp
GCTAAAACATTTATTATAAATTCAGATGATGCAATCCCACTCTTTGATTC
TCGGTTCAGCGTCGGCTATCGGATTAGTTATACCTGCCCATATGGTCAGT
GTGTCTTCATTGGAGGAATCGGCGAGCATACATGTGGTCTCCGTTTTGCC
GCTGTCCTAATCGATCCAGTAGAGCTGGTTGAACCAGCCAATCCGGTAGA
ATTAGCTTTGTTGGACCTTCCATGTTCATCAACCTGGGGTCATCCCGGTC
GAATGAAACCTCGTACTCTGGAGCGAAACCATCGGTACTTGGAATTAATC
TGCTGACAATATCTGCATTCACGCGAGCTAGGTGTCGTCGGGCCAAGTTT
GCTCGCCAGTGGAACGTTTTTTGAGAATCCAGGCAGTATAAACTGATTTC
GGCCCGTTGGCGGGCCTCTCGTGCCGGTTCCTGCCCAGTTCTTTCTTGAT
GGCTACGCTGGGTAGATCTACTTCATCGTTCCGATCTTCAGGTCGACATT
GTCATCTATTCTCCCCATATGTCGCCAGTGAGTATCCATGGTTTTACAGA
GACTGACGGTGTCTTGCTGCCGATTGAGCAGGCACTTGTAAGGTGATCCG
AGAGCCATCCGTCCAATCGCATTTGAGTCTCTTCGATCTAAATATCCATC
GATTTTTAATATCATAATACTAATACGAGTATTTATTGTCGTCATTGGTC
GCTACTTAAAAGAGAACGTATTTTAGAAATAATATACCTCGAGCTTGTTT
TTTCAGAACTACATTCCAGACCTCCTCCAATAGATGTTCGGCGGTTTTTG
GGCCGATCCGTGAACGATACCTCCGCCCTAATATTTTTAATATTTTTCTG
TTAGGCCAAATTTCATACCAGATAGAAGGAA
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protein sequence of SMED30011371-orf-1

>SMED30011371-orf-1 ID=SMED30011371-orf-1|Name=SMED30011371-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
AKTFIINSDDAIPLFDSRFSVGYRISYTCPYGQCVFIGGIGEHTCGLRFA
AVLIDPVELVEPANPVELALLDLPCSSTWGHPGRMKPRTLERNHRYLELI
C*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell