SMED30007186

Overview
NameSMED30007186
Smed IDSMED30007186
Length (bp)898
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 SMED30007186 (SMED30007186) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007186 (SMED30007186) 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




SMED30007186

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007186h1SMcG0020018 SmedASXL_011238SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30007186h1SMcG0020018 dd_Smed_v4_9349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007186h1SMcG0020018 dd_Smed_v4_9349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30007186h1SMcG0020018 dd_Smed_v4_9349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30007186h1SMcG0020018 dd_Smed_v4_9349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30007186h1SMcG0020018 dd_Smed_v4_9349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30007186 vs. Planmine SMEST
Match: SMESG000035193.1 (SMESG000035193.1)

HSP 1 Score: 303.908 bits (777), Expect = 2.654e-101
Identity = 146/152 (96.05%), Postives = 148/152 (97.37%), Query Frame = 3
Query:   27 MNKLLEIINANHALNIKKEDFNSFKLIKPYFDKFLTIIITDSPILVHNLESPDKYLNENGIYPYLPTFYESFQLSDDGYDHVEVIKIARYCSLMQYILDKIDSSSKIKFNFKDVVEPKFSRLVSFLSKLSLFAKFVLATKDTYHQEIQTMAK 482
            MNKLLEIINANHALNIKKEDFNSFKLIKPYFDKFLTIIITDSPILVHNLESPDKYLNENGIYPYLPTFYESFQLSDDGYDHVEVIKIARYCSLMQYILDKIDSSSKIKFNFKDVVEPKFSRLVSFLSKLSLFAKFVLATKDTYHQ ++   K
Sbjct:    1 MNKLLEIINANHALNIKKEDFNSFKLIKPYFDKFLTIIITDSPILVHNLESPDKYLNENGIYPYLPTFYESFQLSDDGYDHVEVIKIARYCSLMQYILDKIDSSSKIKFNFKDVVEPKFSRLVSFLSKLSLFAKFVLATKDTYHQVLRDCEK 152          

HSP 2 Score: 213.772 bits (543), Expect = 3.344e-66
Identity = 123/123 (100.00%), Postives = 123/123 (100.00%), Query Frame = 3
Query:  462 EIQTMAKPEIEINNCLVXXXXXXXXXXXXNSERNQLRLENINKMKSEIKGFEEDIGNFKRELKILERNQRETRKQLKHKEDEVLQINASFKQTNDKYINKMREIERNVEQSLNELKNIYSLKR 830
            EIQTMAKPEIEINNCLVIKREKIIKEIEINSERNQLRLENINKMKSEIKGFEEDIGNFKRELKILERNQRETRKQLKHKEDEVLQINASFKQTNDKYINKMREIERNVEQSLNELKNIYSLKR
Sbjct:  320 EIQTMAKPEIEINNCLVIKREKIIKEIEINSERNQLRLENINKMKSEIKGFEEDIGNFKRELKILERNQRETRKQLKHKEDEVLQINASFKQTNDKYINKMREIERNVEQSLNELKNIYSLKR 442          
The following BLAST results are available for this feature:
BLAST of SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 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 SMED30007186 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000035193.12.654e-10196.05SMESG000035193.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007186 ID=SMED30007186|Name=SMED30007186|organism=Schmidtea mediterranea sexual|type=transcript|length=898bp
TTTTAATTTATTAAGTTAATTTTAAAATGAATAAATTATTAGAAATTATA
AATGCTAATCATGCATTGAATATTAAAAAAGAGGATTTTAACTCATTTAA
ACTTATCAAGCCATATTTTGATAAGTTTCTAACAATAATAATCACAGACT
CTCCAATTCTTGTTCACAATTTAGAAAGTCCCGATAAATATCTTAATGAA
AATGGAATCTATCCATATTTGCCAACATTTTATGAATCATTTCAACTTTC
TGATGATGGTTATGATCATGTCGAAGTGATTAAAATTGCCAGATACTGCA
GCCTTATGCAGTATATTCTAGACAAAATCGATTCAAGTAGTAAAATAAAA
TTCAATTTCAAAGACGTTGTTGAGCCTAAATTCAGTCGATTAGTTTCGTT
TCTTTCTAAATTATCTTTATTTGCAAAATTTGTACTAGCTACAAAAGATA
CTTATCACCAAGAAATTCAAACAATGGCAAAACCGGAAATTGAAATAAAC
AATTGCTTAGTTATAAAGAGAGAAAAAATTATAAAAGAAATAGAAATAAA
CAGCGAAAGAAATCAGTTACGATTAGAAAACATTAACAAAATGAAATCAG
AAATCAAAGGTTTCGAAGAAGACATAGGAAATTTTAAAAGAGAATTGAAG
ATTTTAGAAAGGAATCAACGGGAAACTCGGAAACAGCTTAAGCATAAGGA
GGATGAAGTTTTGCAAATTAATGCGAGCTTTAAGCAAACCAATGATAAAT
ACATCAACAAAATGAGGGAAATCGAACGAAATGTTGAACAGTCTTTAAAT
GAACTGAAAAATATATATTCGTTAAAAAGATAATTGATGATGTTGTTAGG
TATAAATATATTTCGTTCGTTGTTTTTTTTAAGTTATTTCAACCAGAT
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protein sequence of SMED30007186-orf-1

>SMED30007186-orf-1 ID=SMED30007186-orf-1|Name=SMED30007186-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=269bp
MNKLLEIINANHALNIKKEDFNSFKLIKPYFDKFLTIIITDSPILVHNLE
SPDKYLNENGIYPYLPTFYESFQLSDDGYDHVEVIKIARYCSLMQYILDK
IDSSSKIKFNFKDVVEPKFSRLVSFLSKLSLFAKFVLATKDTYHQEIQTM
AKPEIEINNCLVIKREKIIKEIEINSERNQLRLENINKMKSEIKGFEEDI
GNFKRELKILERNQRETRKQLKHKEDEVLQINASFKQTNDKYINKMREIE
RNVEQSLNELKNIYSLKR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: cellular component
TermDefinition
GO:0031262Ndc80 complex
GO:0000776kinetochore
GO:0000775chromosome, centromeric region
Vocabulary: INTERPRO
TermDefinition
IPR005549Kinetochore_Nuf2
Vocabulary: biological process
TermDefinition
GO:0007067mitotic nuclear division
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 186..227
NoneNo IPR availableCOILSCoilCoilcoord: 232..266
IPR005549Kinetochore protein Nuf2PFAMPF03800Nuf2coord: 47..148
e-value: 4.0E-5
score: 23.7