SMED30009462

Overview
NameSMED30009462
Smed IDSMED30009462
Length (bp)341
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 SMED30009462 (SMED30009462) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009462 (SMED30009462) 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



SMED30009462

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30009462SMESG000023794.1 SMESG000022518.1 SmedASXL_019671SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
neoblastSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v4_4051_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30009462SMESG000023794.1 SMESG000022518.1 dd_Smed_v6_4051_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30009462SMESG000023794.1 SMESG000022518.1 OX_Smed_1.0.09482ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30009462SMESG000023794.1 SMESG000022518.1 GU295188smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30009462SMESG000023794.1 SMESG000022518.1 GU295188smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30009462SMESG000023794.1 SMESG000022518.1 GU295188smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009462 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.017799:11972..12268 +1308
Homology
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BLAST of SMED30009462 vs. TrEMBL
Match: E3T7V0 (Secreted peptide prohormone 5 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 114.775 bits (286), Expect = 3.392e-31
Identity = 56/56 (100.00%), Postives = 56/56 (100.00%), Query Frame = -2 
Query:   98 ALDDPEDSLNYYSNYSPAAERSELVSKRGLRILRMGKRNDLFRLLDKRGMRHMRLG 265
            ALDDPEDSLNYYSNYSPAAERSELVSKRGLRILRMGKRNDLFRLLDKRGMRHMRLG
Sbjct:   16 ALDDPEDSLNYYSNYSPAAERSELVSKRGLRILRMGKRNDLFRLLDKRGMRHMRLG 71
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BLAST of SMED30009462 vs. TrEMBL
Match: A0A193PE81 (Neuropeptide-40 (Fragment) OS=Dugesia japonica OX=6161 GN=DjNp40 PE=2 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 5.650e-18
Identity = 40/55 (72.73%), Postives = 46/55 (83.64%), Query Frame = -2 
Query:  101 ALDDPEDSLNYYSNYSPAAERSELVSKRGLRILRMGKRNDLFRLLDKRGMRHMRL 265
            A DD EDSLNY  NY+P + + E V KRGLRILRMGKR++LFRLL+KRGMRHMRL
Sbjct:    3 AHDDTEDSLNYSFNYNPVSAQDENVYKRGLRILRMGKRDELFRLLNKRGMRHMRL 57
The following BLAST results are available for this feature:
BLAST of SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
E3T7V03.392e-31100.00Secreted peptide prohormone 5 OS=Schmidtea mediter... [more]
A0A193PE815.650e-1872.73Neuropeptide-40 (Fragment) OS=Dugesia japonica OX=... [more]
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BLAST of SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 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 SMED30009462 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009462 ID=SMED30009462|Name=SMED30009462|organism=Schmidtea mediterranea sexual|type=transcript|length=341bp
TTTTTTACCTCTACATCGCTTTTATTTAATGAAATAAAATCATAAAAACT
ATTTCAAAGAAAGAAAATTAAATTATTTCGACATTTCTTTGCATTTAACC
CAATCTCATGTGGCGCATTCCTCGTTTATCCAATAACCTGAATAAATCAT
TGCGTTTCCCCATGCGCAGTATTCTCAACCCGCGTTTGCTCACGAGCTCA
CTGCGCTCGGCGGCTGGAGAGTAATTGCTGTAATAATTTAATGAGTCTTC
TGGATCGTCAAGAGCGAATACGAAAACCACGCAAAGAACAATAAATAGAA
GCACTTTCATTTTNTCNNNNGANAAAATCTTTGAAAAAAAA
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Aliases
The feature 'SMED30009462' has the following synonyms
Synonym
spp-5
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000418head
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..26
score: 0.814
NoneNo IPR availableTMHMMTMhelixcoord: 13..27