SMED30030156

Overview
NameSMED30030156
Smed IDSMED30030156
Length (bp)936
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 SMED30030156 (SMED30030156) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030156 (SMED30030156) 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 SMED30030156 (SMED30030156) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030156 (SMED30030156) 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




SMED30030156

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



PAGE Curations: 10

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
anterior sideSMED30030156SMESG000032633.1 dd_Smed_v4_6252_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030156SMESG000032633.1 Contig41065newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030156SMESG000032633.1 Contig41065uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30030156SMESG000032633.1 OX_Smed_1.0.08368ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030156 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014684:2025..12509 +4090
Homology
BLAST of SMED30030156 vs. Planmine SMEST
Match: SMESG000032633.1 (SMESG000032633.1)

HSP 1 Score: 197.593 bits (501), Expect = 1.123e-63
Identity = 128/128 (100.00%), Postives = 128/128 (100.00%), Query Frame = 1
Query:   73 MDCRDHKSILKNPVDEIAICPGYNISTKRASFNDNGILKKIIIDRLNENSLTEDLPNVSSLKESAPVLEVLEETIVSVPXXXXXXXXXXXXXXXXXXXXXXXXXCHERVNIKELLKQTESDFEEDSPE 456
            MDCRDHKSILKNPVDEIAICPGYNISTKRASFNDNGILKKIIIDRLNENSLTEDLPNVSSLKESAPVLEVLEETIVSVPIEDGEEKSNNEEEIERRKLFEEKRKCHERVNIKELLKQTESDFEEDSPE
Sbjct:    1 MDCRDHKSILKNPVDEIAICPGYNISTKRASFNDNGILKKIIIDRLNENSLTEDLPNVSSLKESAPVLEVLEETIVSVPIEDGEEKSNNEEEIERRKLFEEKRKCHERVNIKELLKQTESDFEEDSPE 128          
The following BLAST results are available for this feature:
BLAST of SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 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 SMED30030156 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000032633.11.123e-63100.00SMESG000032633.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030156 ID=SMED30030156|Name=SMED30030156|organism=Schmidtea mediterranea sexual|type=transcript|length=936bp
AATAGCAATCAACTTATAATTTCGATTTTCAAACTACAACATATGAAAAG
ATATATTTTATAATTATTGAAAATGGATTGCCGTGATCACAAAAGTATTT
TAAAAAATCCTGTTGATGAAATAGCTATTTGTCCCGGTTACAATATCTCA
ACGAAAAGGGCGAGTTTCAACGATAATGGAATATTGAAAAAGATTATCAT
AGACAGACTGAATGAGAACAGCTTGACTGAAGATTTACCCAATGTCAGTT
CACTTAAAGAATCAGCTCCTGTTTTGGAAGTTTTGGAAGAAACAATCGTT
TCAGTTCCTATAGAAGATGGTGAGGAAAAATCAAATAATGAAGAAGAAAT
CGAACGAAGAAAGTTGTTCGAAGAAAAACGGAAATGTCATGAAAGGGTAA
ACATTAAAGAGTTATTAAAACAAACTGAATCTGATTTCGAGGAAGATTCT
CCTGAATAAATTTAATGATGATTAATATGCGCATAAGTTATACTATAACC
ATAAATGTAATTTAGAATTCATAGACGCGACCGCAACCTTTTTTAAAAAA
TGTTTTTTTGAATTTTCACTGCATTGTTTAACATTTTAATTTCTTCGGTG
TTTTTATATTGATAATATGATAACTATTGAAATCGAATTTGAAAGTAAGT
AAATTTTTGTTCTGTTTTGAGTGGAGTTCGATATTTCACCTAGAATCATT
TTATTAAATGTGAACTGAATTGGGAACGATTTGATTTATTGATGATATTT
TGAAAACTTATTCGAACTTGTAATAGATATAAATAATTTTTTCTTAAAAA
CTTAAATCAACAATATCATCATATATTTATTATTTTTTGTTTGAAAATTA
TTATTTTGTTGTGGAAATAGTTTGAGGAAAATTTAAATAAAAACCAATTA
TATATTTTGTGATTTAATGAATAAATTAAAACTTTA
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protein sequence of SMED30030156-orf-1

>SMED30030156-orf-1 ID=SMED30030156-orf-1|Name=SMED30030156-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MDCRDHKSILKNPVDEIAICPGYNISTKRASFNDNGILKKIIIDRLNENS
LTEDLPNVSSLKESAPVLEVLEETIVSVPIEDGEEKSNNEEEIERRKLFE
EKRKCHERVNIKELLKQTESDFEEDSPE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR007062PPI-2
Vocabulary: biological process
TermDefinition
GO:0009966regulation of signal transduction
GO:0043666regulation of phosphoprotein phosphatase activity
Vocabulary: molecular function
TermDefinition
GO:0004864protein phosphatase inhibitor activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007062Protein phosphatase inhibitor 2 (IPP-2)PFAMPF04979IPP-2coord: 45..125
e-value: 3.1E-5
score: 24.7