1.C3.2

Overview
Name1.C3.2
Smed IDSMED30018961
Length (bp)675
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 1.C3.2 (SMED30018961) t-SNE clustered cells

Violin plots show distribution of expression levels for 1.C3.2 (SMED30018961) 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 1.C3.2 (SMED30018961) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for 1.C3.2 (SMED30018961) 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



SMED30018961

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018961 dd_Smed_v4_406_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018961 Contig50159newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30018961 Contig50159uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
progenitor cellSMED30018961 dd_Smed_v6_406_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30018961 dd_Smed_v6_406_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30018961 dd_Smed_v6_406_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018961 dd_Smed_v6_406_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
musculature systemSMED30018961 dd_Smed_v6_406_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
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BLAST of 1.C3.2 vs. TrEMBL
Match: V9XQP2 (1.C3.2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 130.183 bits (326), Expect = 2.679e-35
Identity = 66/67 (98.51%), Postives = 66/67 (98.51%), Query Frame = 3 
Query:  150 MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSACLNDKIATSFVTPYCCGVLSMECCYELTV 350
            MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSAC NDKIATSFVTPYCCGVLSMECCYELTV
Sbjct:    1 MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSACSNDKIATSFVTPYCCGVLSMECCYELTV 67
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BLAST of 1.C3.2 vs. Planmine SMEST
Match: SMESG000049306.1 (SMESG000049306.1)

HSP 1 Score: 132.88 bits (333), Expect = 7.625e-40
Identity = 67/67 (100.00%), Postives = 67/67 (100.00%), Query Frame = 3 
Query:  150 MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSACLNDKIATSFVTPYCCGVLSMECCYELTV 350
            MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSACLNDKIATSFVTPYCCGVLSMECCYELTV
Sbjct:    1 MISNIKLIILVLFVSSVKSGDIVNDAIDDLRKLCGSSACLNDKIATSFVTPYCCGVLSMECCYELTV 67
The following BLAST results are available for this feature:
BLAST of 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XQP22.679e-3598.511.C3.2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 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 1.C3.2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000049306.17.625e-40100.00SMESG000049306.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018961 ID=SMED30018961|Name=1.C3.2|organism=Schmidtea mediterranea sexual|type=transcript|length=675bp
ATCGGTTTGAAATTGTATAAACAAAATAATTAGTGAGAATACTTAAACAT
TTTTATTGGACGCACACACCAACANCNNANANNCNNNGAATATTNNNNGA
ATNTAANTNGAATATAAATCGAATCACATGACTTATTTTATTCTGAGAAA
TGATTTCAAATATTAAACTAATAATTTTGGTTCTCTTTGTCTCTAGCGTA
AAATCTGGAGATATAGTCAATGATGCTATAGACGACTTAAGGAAGCTATG
TGGAAGTTCAGCATGTTTGAATGATAAAATTGCAACATCATTTGTCACTC
CGTATTGTTGTGGAGTGTTAAGTATGGAATGTTGTTATGAGCTTACGGTA
TTATCGAAGATTCTTATTGGAGGCATCGTAATAGGCATTATTCTTTCAAT
AATCATATCAATTGCATGCTGCTGTTGTAGTAATAATCGTAGACGCTACT
AATCTCATGTTCTAGGAAGTTTCAATTGAAAAATCTTGATTCGTTAACAA
ATATTTTGAAATTTAATTTCATAAAAATTTTTAAGTTTTTATGATTTTCT
CTATGATTTTACGTGTAATATTTTCTATTATTGTTATTTTAAATAAATTG
TATAGTTATTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000101muscle cell
PLANA:0000120progenitor cell
PLANA:0000428musculature system
PLANA:0000478pharynx musculature
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.838
NoneNo IPR availableTMHMMTMhelixcoord: 71..93