SMED30022058

Overview
NameSMED30022058
Smed IDSMED30022058
Length (bp)803
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 SMED30022058 (SMED30022058) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022058 (SMED30022058) 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.
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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



SMED30022058

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30022058h1SMcG0013362 SmedASXL_003729SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30022058h1SMcG0013362 dd_Smed_v4_5225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022058h1SMcG0013362 dd_Smed_v4_5225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30022058h1SMcG0013362 dd_Smed_v4_5225_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30022058h1SMcG0013362 dd_Smed_v6_5225_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022058 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000311:41505..42295 +3880
Homology
[Close]
BLAST of SMED30022058 vs. Planmine SMEST
Match: SMESG000068601.1 (SMESG000068601.1)

HSP 1 Score: 385.185 bits (988), Expect = 2.188e-137
Identity = 193/209 (92.34%), Postives = 194/209 (92.82%), Query Frame = 1 
Query:   19 MSRMFQRLILLCIFFANQNYGVEFGYKMDYFSNTTYYKINKSGILVPKIDILEEQGIKVLVDPVGKYILLKYQKYNAKVLINETIMKDTERCQKSEIDNRVLFSRIDLFYSHFQQIRTLFKKENPMNSRIFNFDESSYNLQGTTFFSNFWKFNFRAEMDLQDLISTEKAYLISPNRTRIIYEVELKMKFNSLNESDVNELKGLSLSVNC 645
            MSRMFQRLILLCIFFANQNYGVEFGYKMDYFSNTTYYKINKSGILVPKIDILEEQGIKVLVDPV               LINETIMKDTERCQKSEIDNRVLFSRIDLFYSHFQQIRTLFKKENPMNSRIFNFDESSYNLQGTTFFSNFWKFNFRAEM+LQDLISTEKAYLISPNRTRIIYEVELKMKFNSLNESDVNELKGLSLSVNC
Sbjct:    1 MSRMFQRLILLCIFFANQNYGVEFGYKMDYFSNTTYYKINKSGILVPKIDILEEQGIKVLVDPV---------------LINETIMKDTERCQKSEIDNRVLFSRIDLFYSHFQQIRTLFKKENPMNSRIFNFDESSYNLQGTTFFSNFWKFNFRAEMNLQDLISTEKAYLISPNRTRIIYEVELKMKFNSLNESDVNELKGLSLSVNC 194
The following BLAST results are available for this feature:
BLAST of SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 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 SMED30022058 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000068601.12.188e-13792.34SMESG000068601.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022058 ID=SMED30022058|Name=SMED30022058|organism=Schmidtea mediterranea sexual|type=transcript|length=803bp
CCGATCTAAGCTTAAACCATGTCGCGAATGTTCCAACGGTTGATTTTGTT
ATGCATATTCTTTGCAAATCAGAATTACGGTGTGGAATTTGGATATAAAA
TGGACTATTTTTCTAACACAACATATTACAAAATTAATAAATCCGGAATC
CTTGTTCCTAAAATTGATATCCTCGAGGAACAAGGGATAAAGGTCCTAGT
AGATCCGGTAGGTAAATACATATTATTGAAATATCAGAAATATAATGCGA
AGGTTTTAATAAACGAAACAATCATGAAAGATACAGAACGATGTCAAAAA
AGTGAGATTGACAACAGAGTTTTATTTTCCCGAATTGATCTATTCTATTC
GCACTTCCAGCAAATCAGAACATTGTTCAAGAAGGAAAATCCAATGAATT
CACGAATATTTAATTTCGACGAAAGCAGTTATAATCTTCAAGGCACGACA
TTTTTTTCAAATTTTTGGAAATTCAATTTCAGAGCAGAAATGGATTTACA
AGATCTTATTTCCACTGAAAAGGCTTACTTGATTTCACCAAACCGAACAA
GAATCATTTACGAAGTAGAGTTAAAAATGAAATTTAACTCTTTAAATGAA
AGCGATGTTAACGAATTAAAAGGTCTTTCATTGTCAGTTAATTGTTGAAT
TTTGATGAATAAAACCAGAAATCTTTTCAGCTTTAAGAATAAATAGATCT
CAAAAATGACTTTGTTTTTTTAACTTAACTTAATTAATTGTTTTTATATC
TGAAATCTCTATCCAGTGAATTAAAAATATAAATTTTATCTATTAGTGTG
ACC
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protein sequence of SMED30022058-orf-1

>SMED30022058-orf-1 ID=SMED30022058-orf-1|Name=SMED30022058-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=210bp
MSRMFQRLILLCIFFANQNYGVEFGYKMDYFSNTTYYKINKSGILVPKID
ILEEQGIKVLVDPVGKYILLKYQKYNAKVLINETIMKDTERCQKSEIDNR
VLFSRIDLFYSHFQQIRTLFKKENPMNSRIFNFDESSYNLQGTTFFSNFW
KFNFRAEMDLQDLISTEKAYLISPNRTRIIYEVELKMKFNSLNESDVNEL
KGLSLSVNC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
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..21
score: 0.666