SMED30003990

Overview
NameSMED30003990
Smed IDSMED30003990
Length (bp)373
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 SMED30003990 (SMED30003990) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003990 (SMED30003990) 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



SMED30003990

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30003990h1SMcG0013868 PL04009A1F04smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30003990h1SMcG0013868 PL04009A1F04smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30003990h1SMcG0013868 PL04009A1F04smed_ncbi_20240424PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30003990h1SMcG0013868 Contig39374newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003990h1SMcG0013868 Contig39374uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30003990h1SMcG0013868 dd_Smed_v4_4193_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003990h1SMcG0013868 dd_Smed_v4_4193_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
SMED30003990 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000414:159013..159373 -1697
Homology
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BLAST of SMED30003990 vs. Planmine SMEST
Match: SMESG000075965.1 (SMESG000075965.1)

HSP 1 Score: 135.576 bits (340), Expect = 7.015e-38
Identity = 61/62 (98.39%), Postives = 61/62 (98.39%), Query Frame = 2 
Query:  185 MANFSYEIFICFMLICLWLLWNFTKKNRMAAKCLISTDETFNISNETETIAKEPLSFDDIAR 370
            MANFSYEIFICFMLICLWLLWN TKKNRMAAKCLISTDETFNISNETETIAKEPLSFDDIAR
Sbjct:    1 MANFSYEIFICFMLICLWLLWNITKKNRMAAKCLISTDETFNISNETETIAKEPLSFDDIAR 62
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BLAST of SMED30003990 vs. Planmine SMEST
Match: SMESG000075965.1 (SMESG000075965.1)

HSP 1 Score: 73.9442 bits (180), Expect = 2.686e-16
Identity = 34/34 (100.00%), Postives = 34/34 (100.00%), Query Frame = 2 
Query:  269 MAAKCLISTDETFNISNETETIAKEPLSFDDIAR 370
            MAAKCLISTDETFNISNETETIAKEPLSFDDIAR
Sbjct:    1 MAAKCLISTDETFNISNETETIAKEPLSFDDIAR 34
The following BLAST results are available for this feature:
BLAST of SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 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 SMED30003990 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000075965.17.015e-3898.39SMESG000075965.1[more]
SMESG000075965.12.686e-16100.00SMESG000075965.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003990 ID=SMED30003990|Name=SMED30003990|organism=Schmidtea mediterranea sexual|type=transcript|length=373bp
TGGTAATTAAATTTTATCAGTAAAAATTTTCAAGTATGATGAATATTTTT
CAATTAAATAAATTATGATAAGTTGGTATATATATCTTATTTGGAGTTTT
CATTATTTTGCAGAATGTGTGCTAGCTATTTTTTATCTCTTTCTTGGATT
TAGGGTTTTTATTTACTTTTTATTCTTAATTAACATGGCAAATTTCTCTT
ATGAAATTTTTATTTGTTTTATGCTTATTTGTCTGTGGCTGTTGTGGAAT
TTTACTAAGAAAAATCGTATGGCAGCAAAATGTTTGATTTCTACTGATGA
AACTTTCAATATTTCAAATGAAACTGAAACGATAGCGAAAGAACCACTTT
CCTTTGATGATATAGCCCGATAG
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protein sequence of SMED30003990-orf-1

>SMED30003990-orf-1 ID=SMED30003990-orf-1|Name=SMED30003990-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
MISWYIYLIWSFHYFAECVLAIFYLFLGFRVFIYFLFLINMANFSYEIFI
CFMLICLWLLWNFTKKNRMAAKCLISTDETFNISNETETIAKEPLSFDDI
AR*
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 44..63
NoneNo IPR availableTMHMMTMhelixcoord: 7..29