SMED30026176

Overview
NameSMED30026176
Smed IDSMED30026176
Length (bp)398
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 SMED30026176 (SMED30026176) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026176 (SMED30026176) 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



SMED30026176

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30026176SMESG000062603.1 dd_Smed_v4_3069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026176SMESG000062603.1 dd_Smed_v4_3069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026176SMESG000062603.1 dd_Smed_v4_3069_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30026176SMESG000062603.1 dd_3069dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026176 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002483:43982..44607 +1807
Homology
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BLAST of SMED30026176 vs. Planmine SMEST
Match: SMESG000062603.1 (SMESG000062603.1)

HSP 1 Score: 167.933 bits (424), Expect = 2.605e-55
Identity = 85/85 (100.00%), Postives = 85/85 (100.00%), Query Frame = 2 
Query:   80 MLSCSRKHKSNSDYQNRKMYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI 334
            MLSCSRKHKSNSDYQNRKMYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI
Sbjct:    1 MLSCSRKHKSNSDYQNRKMYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI 85
[Close]
BLAST of SMED30026176 vs. Planmine SMEST
Match: SMESG000062603.1 (SMESG000062603.1)

HSP 1 Score: 130.954 bits (328), Expect = 5.667e-41
Identity = 67/67 (100.00%), Postives = 67/67 (100.00%), Query Frame = 2 
Query:  134 MYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI 334
            MYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI
Sbjct:    1 MYILRLIKQRKLKNNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQKRIYI 67
The following BLAST results are available for this feature:
BLAST of SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 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 SMED30026176 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000062603.12.605e-55100.00SMESG000062603.1[more]
SMESG000062603.15.667e-41100.00SMESG000062603.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026176 ID=SMED30026176|Name=SMED30026176|organism=Schmidtea mediterranea sexual|type=transcript|length=398bp
AGAAAGTATAAATTAAAAAAAAATGACTCAACTAAGGCTTGTTTTAATAA
TATTCTTTTTGTCGTTCACAGTTTATCAGATGCTAAGCTGTTCGAGGAAG
CACAAATCAAACTCTGATTACCAGAATAGAAAAATGTATATTTTACGCTT
GATAAAACAGAGAAAATTGAAAAACAATTTTCAAAAAAACAACATCAAGA
CAAATCCAAAGGAACAAAAATTTAAAACAAATAATCCTCCTGAAAAACTT
AGATTTTCAGACAATCCAAAAAATAATGACGGAAAATTAAAGATGAAAAG
GATTTTGTACGGCCTACAGAAACGTATTTATATTTAATTTAAATACAAAA
TTCCAGTTTAATTACATGTGGTTTTAAATTTAATTAATAATTTATTAT
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protein sequence of SMED30026176-orf-1

>SMED30026176-orf-1 ID=SMED30026176-orf-1|Name=SMED30026176-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
MTQLRLVLIIFFLSFTVYQMLSCSRKHKSNSDYQNRKMYILRLIKQRKLK
NNFQKNNIKTNPKEQKFKTNNPPEKLRFSDNPKNNDGKLKMKRILYGLQK
RIYI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 69..87
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 59..87
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..23
score: 0.717
NoneNo IPR availableTMHMMTMhelixcoord: 5..22