SMED30021815

Overview
NameSMED30021815
Smed IDSMED30021815
Length (bp)640
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 SMED30021815 (SMED30021815) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021815 (SMED30021815) 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



SMED30021815

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
nervous systemSMED30021815SMESG000002058.1 dd_Smed_v4_18036_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021815SMESG000002058.1 dd_Smed_v4_18036_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30021815SMESG000002058.1 dd_Smed_v4_18036_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
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BLAST of SMED30021815 vs. Planmine SMEST
Match: SMESG000002058.1 (SMESG000002058.1)

HSP 1 Score: 227.254 bits (578), Expect = 1.103e-75
Identity = 124/132 (93.94%), Postives = 126/132 (95.45%), Query Frame = 2 
Query:  206 RFQAF*KILRDRHIKSLSKKPQRFAAIQFNDFMNPINSGELEISTFFLFYRYTEDCQTRTLKWPLDKIKWYMFSPNSLFSFQCSQSFEPDSHIFKFNCQKCSVMREQLKMQTHXXXXXXXXXXXXFVGGDSI 601
            RF+ F +I    HIKSLSKKPQRFAAIQFNDFMNPINSGELEISTFFLFYRYTEDCQTRTLKWPLDKIKWYMFSPNSLFSFQCSQSFEPDSHIFKFNCQKCSVMREQLKMQTHNLKNLEQNLLENFVGGDSI
Sbjct:   75 RFKRFCEI---EHIKSLSKKPQRFAAIQFNDFMNPINSGELEISTFFLFYRYTEDCQTRTLKWPLDKIKWYMFSPNSLFSFQCSQSFEPDSHIFKFNCQKCSVMREQLKMQTHNLKNLEQNLLENFVGGDSI 203

HSP 2 Score: 161.77 bits (408), Expect = 5.425e-50
Identity = 79/80 (98.75%), Postives = 80/80 (100.00%), Query Frame = 3 
Query:    3 LCWKLEKDNKLENIFKIDNPLYDESKNINELNQMELYQSPDWEEVNKTETKLYSAVFLDKTSRTLDSQDSKRFKRFCEID 242
            LCWKLEKDNKLENIFKIDNPLYDESKNINELNQMELYQSPDWEEVNKTETKLYSAVFLDKTSRTLDSQDSKRFKRFCEI+
Sbjct:    4 LCWKLEKDNKLENIFKIDNPLYDESKNINELNQMELYQSPDWEEVNKTETKLYSAVFLDKTSRTLDSQDSKRFKRFCEIE 83
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BLAST of SMED30021815 vs. Planmine SMEST
Match: SMESG000059045.1 (SMESG000059045.1)

HSP 1 Score: 47.3654 bits (111), Expect = 2.589e-6
Identity = 23/84 (27.38%), Postives = 41/84 (48.81%), Query Frame = 2 
Query:  272 RFAAIQFNDFMNPINSGELEISTFFLFYRYTEDCQTRTLKWPLDKIKWYMFSPNSLFSFQCSQSFEPDSHIFKFNCQKCSVMRE 523
            +F     +D +  I  G L I+T  L + ++ D       WPL  ++WY ++ N +F FQC +        F F+C +  +++E
Sbjct:   63 QFRVSHLDDRLKLIQKGYLGITTNELIFSHSVDITDTIFSWPLTTLRWYAYTHN-MFIFQCGRKSPTGEGTFIFSCNEYQILKE 145
The following BLAST results are available for this feature:
BLAST of SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 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 SMED30021815 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000002058.11.103e-7593.94SMESG000002058.1[more]
SMESG000059045.12.589e-627.38SMESG000059045.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021815 ID=SMED30021815|Name=SMED30021815|organism=Schmidtea mediterranea sexual|type=transcript|length=640bp
ATTTATGTTGGAAACTGGAGAAAGATAACAAACTGGAAAATATATTTAAG
ATTGATAATCCTTTATATGATGAATCAAAAAATATAAATGAGCTAAATCA
AATGGAACTTTATCAATCTCCAGATTGGGAAGAAGTAAATAAGACCGAAA
CAAAGCTTTATAGCGCAGTATTCTTAGATAAAACGAGCAGGACGTTGGAC
AGTCAAGATTCCAAGCGTTTTAAAAGATTCTGCGAGATCGACATATAAAG
TCATTATCAAAGAAACCCCAAAGGTTTGCAGCTATTCAATTCAATGACTT
CATGAACCCAATAAATTCCGGAGAACTGGAAATTAGCACGTTCTTTTTGT
TCTATCGCTATACAGAAGATTGCCAGACTCGTACCTTAAAATGGCCCTTG
GATAAGATCAAGTGGTACATGTTCTCACCAAATTCTTTATTTTCCTTTCA
ATGCAGTCAATCATTTGAACCAGACAGCCATATATTCAAATTCAATTGCC
AGAAATGCTCAGTAATGCGTGAACAGCTGAAAATGCAAACTCACAACTTG
AAGAATTTGGAACAAAATTTGCTGGAAAATTTCGTAGGGGGGGATTCAAT
CTGATTTATTGCAGGGCAAGAGAAGAAATAAATAAATGGC
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protein sequence of SMED30021815-orf-1

>SMED30021815-orf-1 ID=SMED30021815-orf-1|Name=SMED30021815-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MNPINSGELEISTFFLFYRYTEDCQTRTLKWPLDKIKWYMFSPNSLFSFQ
CSQSFEPDSHIFKFNCQKCSVMREQLKMQTHNLKNLEQNLLENFVGGDSI
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: INTERPRO
TermDefinition
IPR011993PH-like_dom_sf