SMED30020679

Overview
NameSMED30020679
Smed IDSMED30020679
Length (bp)786
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30020679 (SMED30020679) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020679 (SMED30020679) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30020679

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30020679h1SMcG0005750 SmedASXL_002319SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X1 cellSMED30020679h1SMcG0005750 SmedASXL_002319SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30020679h1SMcG0005750 SmedASXL_002319SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30020679h1SMcG0005750 Contig37830uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020679h1SMcG0005750 Contig37830newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
cephalic gangliaSMED30020679h1SMcG0005750 dd_Smed_v4_2787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020679h1SMcG0005750 dd_Smed_v4_2787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30020679h1SMcG0005750 dd_Smed_v6_2787_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
zeta neoblastSMED30020679h1SMcG0005750 dd_Smed_v4_2787_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020679h1SMcG0005750 SMED_04153_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020679h1SMcG0005750 SMED_04153_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020679 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002385:54877..55662 -3876
Homology
[Close]
BLAST of SMED30020679 vs. Planmine SMEST
Match: SMESG000007017.1 (SMESG000007017.1)

HSP 1 Score: 42.3578 bits (98), Expect = 3.639e-6
Identity = 27/52 (51.92%), Postives = 35/52 (67.31%), Query Frame = 1 
Query:   16 NLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKI-VEMSKCIKIVKAMD 168
            ++ADR+ +S Q EI NSR  IET LKELVEN K D+I ++     K+ K MD
Sbjct:  180 DIADRIRKSRQDEIENSRRPIETILKELVENSKNDQIKLKGQDLSKLSKVMD 231

HSP 2 Score: 42.3578 bits (98), Expect = 3.639e-6
Identity = 27/52 (51.92%), Postives = 35/52 (67.31%), Query Frame = 1 
Query:   16 NLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKI-VEMSKCIKIVKAMD 168
            ++ADR+ +S Q EI NSR  IET LKELVEN K D+I ++     K+ K MD
Sbjct:  510 DIADRIRKSRQDEIENSRRPIETILKELVENSKNDQIKLKGQDLSKLSKVMD 561

HSP 3 Score: 42.3578 bits (98), Expect = 3.639e-6
Identity = 27/52 (51.92%), Postives = 35/52 (67.31%), Query Frame = 1 
Query:   16 NLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKI-VEMSKCIKIVKAMD 168
            ++ADR+ +S Q EI NSR  IET LKELVEN K D+I ++     K+ K MD
Sbjct:  840 DIADRIRKSRQDEIENSRRPIETILKELVENSKNDQIKLKGQDLSKLSKVMD 891

HSP 4 Score: 42.3578 bits (98), Expect = 3.639e-6
Identity = 27/52 (51.92%), Postives = 35/52 (67.31%), Query Frame = 1 
Query:   16 NLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKI-VEMSKCIKIVKAMD 168
            ++ADR+ +S Q EI NSR  IET LKELVEN K D+I ++     K+ K MD
Sbjct: 1170 DIADRIRKSRQDEIENSRRPIETILKELVENSKNDQIKLKGQDLSKLSKVMD 1221

HSP 5 Score: 42.3578 bits (98), Expect = 3.639e-6
Identity = 27/52 (51.92%), Postives = 35/52 (67.31%), Query Frame = 1 
Query:   16 NLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKI-VEMSKCIKIVKAMD 168
            ++ADR+ +S Q EI NSR  IET LKELVEN K D+I ++     K+ K MD
Sbjct: 1500 DIADRIRKSRQDEIENSRRPIETILKELVENSKNDQIKLKGQDLSKLSKVMD 1551

HSP 6 Score: 26.1794 bits (56), Expect = 3.639e-6
Identity = 11/14 (78.57%), Postives = 11/14 (78.57%), Query Frame = 3 
Query:  177 KSNEMPDAESSNEW 218
            K NE PDAE SNEW
Sbjct:  236 KINETPDAERSNEW 249

HSP 7 Score: 26.1794 bits (56), Expect = 3.639e-6
Identity = 11/14 (78.57%), Postives = 11/14 (78.57%), Query Frame = 3 
Query:  177 KSNEMPDAESSNEW 218
            K NE PDAE SNEW
Sbjct:  566 KINETPDAERSNEW 579

HSP 8 Score: 26.1794 bits (56), Expect = 3.639e-6
Identity = 11/14 (78.57%), Postives = 11/14 (78.57%), Query Frame = 3 
Query:  177 KSNEMPDAESSNEW 218
            K NE PDAE SNEW
Sbjct:  896 KINETPDAERSNEW 909

HSP 9 Score: 26.1794 bits (56), Expect = 3.639e-6
Identity = 11/14 (78.57%), Postives = 11/14 (78.57%), Query Frame = 3 
Query:  177 KSNEMPDAESSNEW 218
            K NE PDAE SNEW
Sbjct: 1226 KINETPDAERSNEW 1239

HSP 10 Score: 26.1794 bits (56), Expect = 3.639e-6
Identity = 11/14 (78.57%), Postives = 11/14 (78.57%), Query Frame = 3 
Query:  177 KSNEMPDAESSNEW 218
            K NE PDAE SNEW
Sbjct: 1556 KINETPDAERSNEW 1569
The following BLAST results are available for this feature:
BLAST of SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 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 SMED30020679 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000007017.13.639e-651.92SMESG000007017.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020679 ID=SMED30020679|Name=SMED30020679|organism=Schmidtea mediterranea sexual|type=transcript|length=786bp
AAGCTGTCGAAATCCAATCTAGCGGACCGAGTTGAAGAGTCTTGGCAAGG
CGAGATTGGGAACAGTCGGTGGTTTATTGAGACAAATCTGAAGGAATTAG
TAGAAAATCCAAAGATTGACAAAATAGTTGAAATGTCAAAATGTATCAAA
ATTGTCAAAGCCATGGATGAAAATGAAAGAGTAATGAAATGCCAGATGCT
GAAAGCTCGAATGAATGGAATGACAAACAGGAGCAGGATATTAGAAATTG
AGAAAAAACCATATCGGAGAACAAGTTGTTTGGATCCACCAAGATATTTT
CAAGTGGAGACGACTTGTTCTCTGAATTATCAAAACTGCTGCTCAAAATA
AATTTCAACAAAGTTTCAAAATCTTTATTTTTTCCAAATAAAATAACAAA
TTCAATGAAACAGATAAATTCGATAATTAATAATTCACAGGGCTCAAATA
ACGCGTACGCAGACGCGATACAAAATTCTAGACACAGTAACAATCAAACG
CAGATGAGAATAAAGTGCAGGAACCAAATTCTCACACAAAGTTTTGATTT
CAGGACTGACCATCCAATCAAAAAAGCAATACAACTGTCTATTTAAGATA
AATTATACATAAATTAAATAGGAAAAATGTTAGAAAAATATTTTTGCTAG
GGCCTCCAAATATGTAAAGTTGGCCCTGTTTGACAGAGAGGGAATGAGAT
TAAATTGCTCATTGACAACAGATCTCCCGTTCCTATGTTATCGGATTGAT
ATTGTTGTGCAGGAACGCCTAATCACCAAAGTCACT
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protein sequence of SMED30020679-orf-1

>SMED30020679-orf-1 ID=SMED30020679-orf-1|Name=SMED30020679-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
KLSKSNLADRVEESWQGEIGNSRWFIETNLKELVENPKIDKIVEMSKCIK
IVKAMDENERVMKCQMLKARMNGMTNRSRILEIEKKPYRRTSCLDPPRYF
QVETTCSLNYQNCCSK*
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