SMED30020349

Overview
NameSMED30020349
Smed IDSMED30020349
Length (bp)796
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 SMED30020349 (SMED30020349) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020349 (SMED30020349) 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




SMED30020349

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermal cellSMED30020349SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020349SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30020349SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020349 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006515:15965..20312 -3942
Homology
BLAST of SMED30020349 vs. Planmine SMEST
Match: SMESG000043379.1 (SMESG000043379.1)

HSP 1 Score: 343.199 bits (879), Expect = 2.331e-112
Identity = 201/204 (98.53%), Postives = 203/204 (99.51%), Query Frame = 2
Query:  185 MMQVSIVQYALTFNFQKDIPDQTNLAVSDSVSAIYIPDQIYVTNIINSDGSVSPSGFILESLNSILIPIKLSYSLSLTGVTTIGRLTKFGFTGLLGQLNMNASDMIGIPVLFEPSYLNRFIYSQKIFVVPYSILMKQSTKGLNLPRLAEPFSPIVWXXXXXXXXXXXXXXXXXXXXXXXXADPTQKLTVSNSIFMVIGSFLMAK 796
            ++ VSIVQYALTFNFQKDIPDQTNLAVSDSVSAIYIPDQIYVTNIINSDGSVSPSGFILESLNSILIPIKLSYSLSLTGVTTIGRLTKFGFTGLLGQLNMNASDMIGIPVLFEPSYLNRFIYSQKIFVVPYSILMKQSTKGLNLPRLAEPFSPIVWLVIIVTIIFLSIILWLINLISPNIADPTQKLTVSNSIFMVIGSFLMAK
Sbjct:  324 LLPVSIVQYALTFNFQKDIPDQTNLAVSDSVSAIYIPDQIYVTNIINSDGSVSPSGFILESLNSILIPIKLSYSLSLTGVTTIGRLTKFGFTGLLGQLNMNASDMIGIPVLFEPSYLNRFIYSQKIFVVPYSILMKQSTKGLNLPRLAEPFSPIVWLVIIVTIIFLSIILWLINLISPNIADPTQKLTVSNSIFMVIGSFLMAK 527          

HSP 2 Score: 136.732 bits (343), Expect = 3.659e-36
Identity = 63/64 (98.44%), Postives = 64/64 (100.00%), Query Frame = 2
Query:    2 SDAMEILWGLTGKTIKQCNFLMTDNDTNIAGCFQNLNLVSTPGRAYIFVTSDENSSLLDKIMMQ 193
            S+AMEILWGLTGKTIKQCNFLMTDNDTNIAGCFQNLNLVSTPGRAYIFVTSDENSSLLDKIMMQ
Sbjct:  148 SNAMEILWGLTGKTIKQCNFLMTDNDTNIAGCFQNLNLVSTPGRAYIFVTSDENSSLLDKIMMQ 211          
The following BLAST results are available for this feature:
BLAST of SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 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 SMED30020349 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000043379.12.331e-11298.53SMESG000043379.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020349 ID=SMED30020349|Name=SMED30020349|organism=Schmidtea mediterranea sexual|type=transcript|length=796bp
TTCAGATGCTATGGAGATTTTATGGGGCCTAACAGGGAAGACTATTAAGC
AATGTAACTTCCTTATGACAGATAATGATACAAATATCGCTGGATGTTTT
CAAAACCTCAATTTGGTCAGTACTCCTGGACGGGCTTATATATTTGTAAC
TTCTGACGAGAATTCAAGCTTGTTAGATAAAATAATGATGCAAGTTTCAA
TAGTACAATACGCACTGACTTTTAACTTCCAAAAAGATATTCCGGATCAA
ACTAATCTCGCTGTTTCGGATTCCGTTTCAGCAATCTACATACCAGATCA
GATATATGTGACTAATATTATTAATTCCGATGGATCAGTTTCACCGTCTG
GGTTCATTTTAGAATCTCTGAATTCAATTCTAATTCCCATCAAATTGTCA
TACTCCTTGTCACTCACAGGTGTTACAACCATTGGAAGACTTACAAAGTT
TGGCTTTACTGGGCTGTTGGGTCAATTGAATATGAATGCAAGCGATATGA
TTGGGATTCCGGTTCTTTTCGAGCCGTCTTATTTAAATAGATTTATATAC
TCCCAGAAGATATTTGTTGTTCCATATTCGATTTTGATGAAACAGAGTAC
AAAAGGATTGAACCTCCCAAGACTTGCTGAACCTTTTTCCCCGATAGTCT
GGCTTGTTATCATAGTGACCATAATATTTCTCAGTATCATTCTATGGTTG
ATCAATTTAATCAGTCCAAATATCGCCGATCCAACACAGAAGCTTACAGT
CAGTAACAGCATTTTCATGGTTATTGGATCTTTTCTGATGGCAAAG
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protein sequence of SMED30020349-orf-1

>SMED30020349-orf-1 ID=SMED30020349-orf-1|Name=SMED30020349-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=265bp
SDAMEILWGLTGKTIKQCNFLMTDNDTNIAGCFQNLNLVSTPGRAYIFVT
SDENSSLLDKIMMQVSIVQYALTFNFQKDIPDQTNLAVSDSVSAIYIPDQ
IYVTNIINSDGSVSPSGFILESLNSILIPIKLSYSLSLTGVTTIGRLTKF
GFTGLLGQLNMNASDMIGIPVLFEPSYLNRFIYSQKIFVVPYSILMKQST
KGLNLPRLAEPFSPIVWLVIIVTIIFLSIILWLINLISPNIADPTQKLTV
SNSIFMVIGSFLMAK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.10.287.70coord: 201..263
e-value: 5.3E-14
score: 53.8
NoneNo IPR availableGENE3DG3DSA:3.40.190.10coord: 191..200
e-value: 5.3E-14
score: 53.8
NoneNo IPR availableGENE3DG3DSA:3.40.190.10coord: 116..190
e-value: 5.3E-14
score: 53.8
NoneNo IPR availableTMHMMTMhelixcoord: 215..237