SMED30016092

Overview
NameSMED30016092
Smed IDSMED30016092
Length (bp)361
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 SMED30016092 (SMED30016092) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016092 (SMED30016092) in cells (dots) of each of the 12 neoblast clusters.

 

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Anatomical Expression

PAGE et. al., 2020



SMED30016092

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30016092 dd_Smed_v4_3534_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30016092 dd_Smed_v6_3534_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
musculature systemSMED30016092 dd_Smed_v6_3534_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 SMED30016092 vs. Planmine SMEST
Match: SMESG000079932.1 (SMESG000079932.1)

HSP 1 Score: 74.3294 bits (181), Expect = 2.985e-17
Identity = 38/58 (65.52%), Postives = 44/58 (75.86%), Query Frame = -2 
Query:   25 GYAPPYNTSFNLDDPRLDGRSTAINVIVPRKILPRDLRIEEDRLDGHLENHYARERSE 198
            GYAPPYNTS+NLDD RL+ RSTAINV+VP+KILPR +R  E   D H E+ YA   SE
Sbjct:   90 GYAPPYNTSYNLDDERLNIRSTAINVVVPQKILPRHMRRTEKPADEHREHPYAWPVSE 147
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BLAST of SMED30016092 vs. Planmine SMEST
Match: SMESG000057616.1 (SMESG000057616.1)

HSP 1 Score: 71.633 bits (174), Expect = 4.418e-16
Identity = 34/54 (62.96%), Postives = 43/54 (79.63%), Query Frame = -2 
Query:   37 GYAPPYNTSFNLDDPRLDGRSTAINVIVPRKILPRDLRIEEDRLDGHLENHYAR 198
            GYAPPYNTSFNLDD RL+  S A++V+VPR+IL RD+R  ++R D H E+ YAR
Sbjct:  100 GYAPPYNTSFNLDDRRLNTNSKAVDVVVPRRILSRDMRAGKERNDEHREHPYAR 153
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BLAST of SMED30016092 vs. Planmine SMEST
Match: SMESG000039041.1 (SMESG000039041.1)

HSP 1 Score: 72.0182 bits (175), Expect = 7.108e-16
Identity = 33/54 (61.11%), Postives = 43/54 (79.63%), Query Frame = -2 
Query:   37 GYAPPYNTSFNLDDPRLDGRSTAINVIVPRKILPRDLRIEEDRLDGHLENHYAR 198
            GYAP YNTSFNLDD RL+  S  INV+VP +ILPR++R E++++D H E+ YAR
Sbjct:  130 GYAPSYNTSFNLDDRRLNTNSKTINVVVPWRILPRNMRTEKEQIDEHREHPYAR 183
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BLAST of SMED30016092 vs. Planmine SMEST
Match: SMESG000029442.1 (SMESG000029442.1)

HSP 1 Score: 67.3958 bits (163), Expect = 3.834e-15
Identity = 32/59 (54.24%), Postives = 43/59 (72.88%), Query Frame = -2 
Query:   19 YAPPYNTSFNLDDPRLDGRSTAINVIVPRKILPRDLRIEEDRLDGHLENHYARERSEER 195
            YAP YN SF LDDPRL G++ A+NV+VPR++LPR+LR  E++ D   ++ YAR R   R
Sbjct:   91 YAPNYNVSFELDDPRLRGQTGAMNVVVPRRVLPRELRNVEEKPDHRYDHSYARSRPSRR 149
[Close]
BLAST of SMED30016092 vs. Planmine SMEST
Match: SMESG000066467.1 (SMESG000066467.1)

HSP 1 Score: 69.707 bits (169), Expect = 7.152e-15
Identity = 36/76 (47.37%), Postives = 47/76 (61.84%), Query Frame = -2 
Query:    1 GYAPPYNTSFNLDDPRLDGRSTAINVIVPRKILPRDLRIEEDRLDGHLENHYAR----------ERSEERFSRNAE 198
            GYAPPYNTSFNLDD RL+  + A+NV++PRK LPR +R  E   + H E+ YAR           R  + +S+N E
Sbjct:  329 GYAPPYNTSFNLDDERLNVNAEAMNVVIPRKALPRKMRRNEGPAERHNEHPYARTVSKSDSFQHHRKTDHYSKNLE 404
The following BLAST results are available for this feature:
BLAST of SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 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 SMED30016092 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000079932.12.985e-1765.52SMESG000079932.1[more]
SMESG000057616.14.418e-1662.96SMESG000057616.1[more]
SMESG000039041.17.108e-1661.11SMESG000039041.1[more]
SMESG000029442.13.834e-1554.24SMESG000029442.1[more]
SMESG000066467.17.152e-1547.37SMESG000066467.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016092 ID=SMED30016092|Name=SMED30016092|organism=Schmidtea mediterranea sexual|type=transcript|length=361bp
CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTTTCTCGAGCATAATGGT
TCTCGAGGTGGCCATCGAGTCGGTCTTCTTCTATCCTCAAGTCACGGGGA
AGTATCTTCCGTGGGACTATCACGTTGATTGCCGTAGACCTCCCATCTAA
TCTAGGGTCGTCAAGATTAAATGAGGTATTGTACGGGGGAGCATATCCTA
CGGGGGGCATGTCCTATCGCTTATCTGAACGGTGATAAGCACCGTAAGGG
GCGACGTTTATGGAGGCTACGAAGTCGTCATTTGCTTGCGATTTCGCTAT
CTTGTAATTTTCTGAGTTCCGATCCCGAGTGGGGCAAAGTGCGTAATCAA
CGGCCTTACTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000428musculature system
PLANA:0000478pharynx musculature