SMED30027151

Overview
NameSMED30027151
Smed IDSMED30027151
Length (bp)300
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30027151

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
posterior region of the whole animalSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:27063937
Scimone et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30027151h1SMcG0002271 SmedASXL_015764SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30027151h1SMcG0002271 dd_Smed_v4_13356_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30027151h1SMcG0002271 dd_Smed_v6_13356_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
SMED30027151 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002042:16016..16315 -1500
v31.020609:8578..8877 -1473
Homology
BLAST of SMED30027151 vs. Planmine SMEST
Match: SMESG000037981.1 (SMESG000037981.1)

HSP 1 Score: 171.014 bits (432), Expect = 5.468e-52
Identity = 97/97 (100.00%), Postives = 97/97 (100.00%), Query Frame = 3
Query:    9 MPHLFFAISLCIILLQIHSYTNRKCTKESKKHFYCRNDFFDLSSSKELIAEDYLLKFKIQIKTYKSFQNHXXXXXXXXXXXXXQDPLCDPITNIRLG 299
            MPHLFFAISLCIILLQIHSYTNRKCTKESKKHFYCRNDFFDLSSSKELIAEDYLLKFKIQIKTYKSFQNHKCIKTLITLLCLIQDPLCDPITNIRLG
Sbjct:    1 MPHLFFAISLCIILLQIHSYTNRKCTKESKKHFYCRNDFFDLSSSKELIAEDYLLKFKIQIKTYKSFQNHKCIKTLITLLCLIQDPLCDPITNIRLG 97          
The following BLAST results are available for this feature:
BLAST of SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 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 SMED30027151 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000037981.15.468e-52100.00SMESG000037981.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027151 ID=SMED30027151|Name=SMED30027151|organism=Schmidtea mediterranea sexual|type=transcript|length=300bp
ATTGTGAAATGCCTCACTTGTTCTTTGCAATTAGTTTGTGTATTATTTTA
TTACAAATCCATTCCTATACTAACCGAAAATGTACCAAAGAATCAAAAAA
GCACTTTTATTGTCGAAATGACTTCTTTGACCTTTCTAGTTCAAAAGAAC
TCATCGCCGAGGACTATTTATTGAAATTTAAAATTCAAATTAAGACTTAC
AAATCCTTTCAAAATCATAAATGCATTAAAACTTTAATTACCCTTCTCTG
TTTAATCCAGGATCCACTTTGTGATCCCATTACCAACATCCGACTCGGAC
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protein sequence of SMED30027151-orf-1

>SMED30027151-orf-1 ID=SMED30027151-orf-1|Name=SMED30027151-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=99bp
CEMPHLFFAISLCIILLQIHSYTNRKCTKESKKHFYCRNDFFDLSSSKEL
IAEDYLLKFKIQIKTYKSFQNHKCIKTLITLLCLIQDPLCDPITNIRLG
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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: 0.692
NoneNo IPR availableTMHMMTMhelixcoord: 5..22