SMED30019575

Overview
NameSMED30019575
Smed IDSMED30019575
Length (bp)412
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30019575 (SMED30019575) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30019575 (SMED30019575) 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.
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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



SMED30019575

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



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30019575SMESG000032456.1 SMESG000032323.1 Contig697newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30019575SMESG000032456.1 SMESG000032323.1 Contig697uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30019575SMESG000046951.1 Contig697newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30019575SMESG000046951.1 Contig697uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30019575SMESG000032456.1 SMESG000032323.1 Contig697newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019575SMESG000032456.1 SMESG000032323.1 Contig697uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019575SMESG000032467.1 SMESG000032456.1 SMESG000032323.1 Contig3891newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019575SMESG000032467.1 SMESG000032456.1 SMESG000032323.1 Contig3891uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019575SMESG000046951.1 Contig697newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019575SMESG000046951.1 Contig697uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30019575 dd_Smed_v4_11953_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30019575 dd_Smed_v4_11953_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30019575 dd_Smed_v4_11953_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019575 dd_Smed_v4_11953_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30019575 dd_Smed_v4_11953_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019575 dd_Smed_v6_11953_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30019575 vs. Planmine SMEST
Match: SMESG000032323.1 (SMESG000032323.1)

HSP 1 Score: 64.3142 bits (155), Expect = 8.664e-22
Identity = 29/59 (49.15%), Postives = 42/59 (71.19%), Query Frame = 1 
Query:   52 NLCENGMKWKTI---VKLNLSPQFNALIVLQKSESGCAISPQCQDCQSAKRIIGETFEG 219
            NLCE+G+ W+T    VKL +  +F+ + +LQKSES CAIS QC+ C+S +++IG  F G
Sbjct:   76 NLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRTCRSVEQMIGNLFNG 134

HSP 2 Score: 42.3578 bits (98), Expect = 8.664e-22
Identity = 19/45 (42.22%), Postives = 28/45 (62.22%), Query Frame = 3 
Query:  219 CQRLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKFD 353
            CQ L++  + T S+SF NL H ++Y FYIL  + G+   F FK +
Sbjct:  135 CQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKLN 179

HSP 3 Score: 33.4982 bits (75), Expect = 8.664e-22
Identity = 15/18 (83.33%), Postives = 17/18 (94.44%), Query Frame = 2 
Query:  359 SNGYSLAVSGHFTKSFNT 412
            ++GYSLAVSGH TKSFNT
Sbjct:  219 TSGYSLAVSGHSTKSFNT 236
[Close]
BLAST of SMED30019575 vs. Planmine SMEST
Match: SMESG000032323.1 (SMESG000032323.1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.479e-21
Identity = 29/59 (49.15%), Postives = 42/59 (71.19%), Query Frame = 1 
Query:   52 NLCENGMKWKTI---VKLNLSPQFNALIVLQKSESGCAISPQCQDCQSAKRIIGETFEG 219
            NLCE+G+ W+T    VKL +  +F+ + +LQKSES CAIS QC+ C+S +++IG  F G
Sbjct:   90 NLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRTCRSVEQMIGNLFNG 148

HSP 2 Score: 42.3578 bits (98), Expect = 1.479e-21
Identity = 19/45 (42.22%), Postives = 28/45 (62.22%), Query Frame = 3 
Query:  219 CQRLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKFD 353
            CQ L++  + T S+SF NL H ++Y FYIL  + G+   F FK +
Sbjct:  149 CQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKLN 193

HSP 3 Score: 33.8834 bits (76), Expect = 1.479e-21
Identity = 15/18 (83.33%), Postives = 17/18 (94.44%), Query Frame = 2 
Query:  359 SNGYSLAVSGHFTKSFNT 412
            ++GYSLAVSGH TKSFNT
Sbjct:  233 TSGYSLAVSGHSTKSFNT 250
[Close]
BLAST of SMED30019575 vs. Planmine SMEST
Match: SMESG000032323.1 (SMESG000032323.1)

HSP 1 Score: 62.7734 bits (151), Expect = 1.671e-21
Identity = 29/59 (49.15%), Postives = 42/59 (71.19%), Query Frame = 1 
Query:   52 NLCENGMKWKTI---VKLNLSPQFNALIVLQKSESGCAISPQCQDCQSAKRIIGETFEG 219
            NLCE+G+ W+T    VKL +  +F+ + +LQKSES CAIS QC+ C+S +++IG  F G
Sbjct:   90 NLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRTCRSVEQMIGNLFNG 148

HSP 2 Score: 42.3578 bits (98), Expect = 1.671e-21
Identity = 19/45 (42.22%), Postives = 28/45 (62.22%), Query Frame = 3 
Query:  219 CQRLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKFD 353
            CQ L++  + T S+SF NL H ++Y FYIL  + G+   F FK +
Sbjct:  149 CQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKLN 193

HSP 3 Score: 33.4982 bits (75), Expect = 1.671e-21
Identity = 15/18 (83.33%), Postives = 17/18 (94.44%), Query Frame = 2 
Query:  359 SNGYSLAVSGHFTKSFNT 412
            ++GYSLAVSGH TKSFNT
Sbjct:  233 TSGYSLAVSGHSTKSFNT 250
[Close]
BLAST of SMED30019575 vs. Planmine SMEST
Match: SMESG000032456.1 (SMESG000032456.1)

HSP 1 Score: 63.1586 bits (152), Expect = 2.550e-17
Identity = 29/59 (49.15%), Postives = 42/59 (71.19%), Query Frame = 1 
Query:   52 NLCENGMKWKTI---VKLNLSPQFNALIVLQKSESGCAISPQCQDCQSAKRIIGETFEG 219
            NLCE+G+ W+T    VKL +  +F+ + +LQKSES CAIS QC+ C+S +++IG  F G
Sbjct:   80 NLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRMCRSVEQMIGNLFNG 138

HSP 2 Score: 41.9726 bits (97), Expect = 2.550e-17
Identity = 19/44 (43.18%), Postives = 27/44 (61.36%), Query Frame = 3 
Query:  219 CQRLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKF 350
            CQ L++  + T S+SF NL H ++Y FYIL  + G+   F FK 
Sbjct:  139 CQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKL 182
[Close]
BLAST of SMED30019575 vs. Planmine SMEST
Match: SMESG000032456.1 (SMESG000032456.1)

HSP 1 Score: 62.003 bits (149), Expect = 3.798e-17
Identity = 29/59 (49.15%), Postives = 42/59 (71.19%), Query Frame = 1 
Query:   52 NLCENGMKWKTI---VKLNLSPQFNALIVLQKSESGCAISPQCQDCQSAKRIIGETFEG 219
            NLCE+G+ W+T    VKL +  +F+ + +LQKSES CAIS QC+ C+S +++IG  F G
Sbjct:   94 NLCEDGISWETFEKSVKLKIPNKFDTVTILQKSESECAISAQCRMCRSVEQMIGNLFNG 152

HSP 2 Score: 42.3578 bits (98), Expect = 3.798e-17
Identity = 19/44 (43.18%), Postives = 27/44 (61.36%), Query Frame = 3 
Query:  219 CQRLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKF 350
            CQ L++  + T S+SF NL H ++Y FYIL  + G+   F FK 
Sbjct:  153 CQLLEVSRDHTRSISFPNLLHSTKYHFYILPIQEGRLMGFVFKL 196
The following BLAST results are available for this feature:
BLAST of SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 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 SMED30019575 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000032323.18.664e-2249.15SMESG000032323.1[more]
SMESG000032323.11.479e-2149.15SMESG000032323.1[more]
SMESG000032323.11.671e-2149.15SMESG000032323.1[more]
SMESG000032456.12.550e-1749.15SMESG000032456.1[more]
SMESG000032456.13.798e-1749.15SMESG000032456.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019575 ID=SMED30019575|Name=SMED30019575|organism=Schmidtea mediterranea sexual|type=transcript|length=412bp
CAAGATATTGGTGTTCTGTTACAGCAAAACGTATAATTAGCAAAATTAGA
TAATTTATGTGAAAATGGGATGAAATGGAAGACAATTGTCAAGTTGAACC
TTTCTCCTCAATTCAATGCGTTAATTGTTTTACAGAAATCCGAATCAGGA
TGCGCAATATCCCCCCAATGTCAAGATTGTCAATCGGCCAAAAGAATAAT
TGGAGAGACCTTCGAAGGTGTCAACGTTTGAAGATCATTAGCAATTCTAC
AGAGTCAGTTTCATTTGACAACCTGAAACACAAATCTCGGTATCTTTTCT
ATATTCTATCTACAAAAAATGGACAATGGAAAGAGTTTTTTTTTAAGTTT
GACAATAAAGCAACGGATATTCACTAGCAGTCTCGGGCCATTTCACAAAA
TCCTTCAATACA
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protein sequence of SMED30019575-orf-1

>SMED30019575-orf-1 ID=SMED30019575-orf-1|Name=SMED30019575-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MEDNCQVEPFSSIQCVNCFTEIRIRMRNIPPMSRLSIGQKNNWRDLRRCQ
RLKIISNSTESVSFDNLKHKSRYLFYILSTKNGQWKEFFFKFDNKATDIH
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0003116parenchymal cell