SMED30002134

Overview
NameSMED30002134
Smed IDSMED30002134
Length (bp)616
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

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 SMED30002134 (SMED30002134) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30002134 (SMED30002134) in cells (dots) of each of the 12 neoblast clusters.

 

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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 SMED30002134 (SMED30002134) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002134 (SMED30002134) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30002134

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



PAGE Curations: 26

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 2 cellSMED30002134h1SMcG0005535 NB.32.1gsmed_ncbi_20240424PMID:24704339
Vogg et al., 2014		whole organism asexual adult fluorescence in situ hybridization evidence
pigment cellSMED30002134h1SMcG0005535 SmedASXL_073532SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
Category 2 cellSMED30002134h1SMcG0005535 SMED30002134smed_20140614PMID:26114597
Zhu et al., 2015		whole organism asexual adult fluorescence in situ hybridization evidence
parenchymaSMED30002134h1SMcG0005535 SMED30002134smed_20140614PMID:26114597
Zhu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
X1 cellSMED30002134h1SMcG0005535 SmedASXL_073532SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30002134h1SMcG0005535 SmedASXL_073532SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30002134h1SMcG0005535 Contig56GPL15192PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002134h1SMcG0005535 Contig44156uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002134h1SMcG0005535 Contig44156newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30002134h1SMcG0005543 dd_Smed_v6_69_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30002134h1SMcG0005535 dd_Smed_v6_69_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30002134h1SMcG0005535 dd_Smed_v4_69_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30002134h1SMcG0005535 NB.32.1gsmed_ncbi_20240424PMID:18786419
Eisenhoffer et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
Category 2 cellSMED30002134h1SMcG0005535 NB.32.1gsmed_ncbi_20240424PMID:18786419
Eisenhoffer et al., 2008		whole organism asexual adult cDNA to DNA expression microarray evidence
Category 2 cellSMED30002134h1SMcG0005535 DN306632smed_ncbi_20240424PMID:23235145
Hubert et al., 2013		whole organism asexual adult colorimetric in situ hybridization evidence
Category 2 cellSMED30002134h1SMcG0005535 DN298711smed_ncbi_20240424PMID:23235145
Hubert et al., 2013		whole organism asexual adult colorimetric in situ hybridization evidence
Category 2 cellSMED30002134h1SMcG0005535 NB.32.1gsmed_ncbi_20240424PMID:25956527
Henderson et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002134 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.012923:3741..4413 -2923
v31.027295:3894..4566 -2896
v31.010791:11802..12471 -2313
Homology
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BLAST of SMED30002134 vs. Planmine SMEST
Match: SMESG000054781.1 (SMESG000054781.1)

HSP 1 Score: 226.868 bits (577), Expect = 6.316e-77
Identity = 113/115 (98.26%), Postives = 113/115 (98.26%), Query Frame = -2 
Query:   28 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 372
            MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRD  VKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA
Sbjct:    1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 115
[Close]
BLAST of SMED30002134 vs. Planmine SMEST
Match: SMESG000025013.1 (SMESG000025013.1)

HSP 1 Score: 226.868 bits (577), Expect = 6.316e-77
Identity = 113/115 (98.26%), Postives = 113/115 (98.26%), Query Frame = -2 
Query:   28 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 372
            MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRD  VKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA
Sbjct:    1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 115
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BLAST of SMED30002134 vs. Planmine SMEST
Match: SMESG000025003.1 (SMESG000025003.1)

HSP 1 Score: 221.861 bits (564), Expect = 6.773e-75
Identity = 111/113 (98.23%), Postives = 112/113 (99.12%), Query Frame = -2 
Query:   28 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 366
            LDKIQKREMSAECQGELQKLRDGFDKATDELDKKC+SQYNELRKKAETAYMANLRKCGDNIKDFSKECRD LVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA
Sbjct:    9 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCKSQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGLVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 121
[Close]
BLAST of SMED30002134 vs. Planmine SMEST
Match: SMESG000024991.1 (SMESG000024991.1)

HSP 1 Score: 134.42 bits (337), Expect = 1.668e-40
Identity = 74/115 (64.35%), Postives = 85/115 (73.91%), Query Frame = -2 
Query:   28 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 372
            MRLDKIQKREMSAEC GELQKLRD F KATDELDKKCESQY + + K    Y  N +KC + I   ++ECR  + + +  + EE +KINNACENE R LLEELN N DNLKKKCA
Sbjct:    1 MRLDKIQKREMSAECLGELQKLRDDFAKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIP-MTQECRKGITQISIRYGEEIQKINNACENEYRKLLEELNANEDNLKKKCA 114
[Close]
BLAST of SMED30002134 vs. Planmine SMEST
Match: SMESG000025000.1 (SMESG000025000.1)

HSP 1 Score: 95.5153 bits (236), Expect = 4.006e-25
Identity = 52/137 (37.96%), Postives = 84/137 (61.31%), Query Frame = -2 
Query:   28 MAKLIFIVLAVLFVYGECRRFKMRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNKNVDNLKKKCA 438
            M K++ +   + FV  ECR F++RLDKI KREMS+EC+ EL+KL D F  A +++D  C++ Y +  KK    Y+A   KCG +    +K+C+  L +    F+E + K++  C+NE   L+ + +K  + LK++CA
Sbjct:    1 MNKILLLTFVIFFVSVECR-FRLRLDKIAKREMSSECKAELKKLDDQFTAAANKIDDDCDAVYVKWSKKYLPEYVALKEKCGLDTSKMTKDCKTELKRLFNLFAEGNYKVDLECDNEYAALVRQTSKEKEKLKQQCA 136
The following BLAST results are available for this feature:
BLAST of SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 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 SMED30002134 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054781.16.316e-7798.26SMESG000054781.1[more]
SMESG000025013.16.316e-7798.26SMESG000025013.1[more]
SMESG000025003.16.773e-7598.23SMESG000025003.1[more]
SMESG000024991.11.668e-4064.35SMESG000024991.1[more]
SMESG000025000.14.006e-2537.96SMESG000025000.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002134 ID=SMED30002134|Name=SMED30002134|organism=Schmidtea mediterranea sexual|type=transcript|length=616bp
ATCAACGAAATCATTTTACTGAATTTATGCACATTTCTTTTTCAAATTAT
CTACATTTTTATTCAATTCTTCTAAAAGTATTCGACTTTCATTTTCACAC
GCATTGTTTATTTTTTCGTCTTCTTCACTGAACCATTTTGTGTGCTTTAC
AAGGGCATCGCGACATTCCTTTGAAAAATCTTTAATATTATCACCACATT
TCCTCAAATTTGCCATGTAAGCTGTTTCAGCCTTTTTTCTTAATTCGTTA
TATTGACTTTCACATTTTTTATCGAGCTCGTCCGTAGCTTTGTCGAAACC
ATCGCGCAACTTTTGCAGTTCTCCTTGACATTCGGCACTCATTTCTCGTT
TCTGTATTTTGTCGAGTCGCATTTTAAATCGGCGGCATTCTCCGTAAACA
AATAACACAGCGAGAACAATAAAAATTAATTTTGCCATTATGAAATAGTT
AAAGAAAAACATTTTTCTCAAATATTTATAGTTGGAGCTGACGAACAGAA
GAGACATGCGAGTTACGGTTGATGAGCAAACCCAATGTAACCCGTTCTAG
TTCCAGAAAGCTTATCAATGATTTTATTATAAAGTTTTAAACAGGTCCAA
ACATTCTTGTACGTTT
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protein sequence of SMED30002134-orf-1

>SMED30002134-orf-1 ID=SMED30002134-orf-1|Name=SMED30002134-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=161bp
MSLLFVSSNYKYLRKMFFFNYFIMAKLIFIVLAVLFVYGECRRFKMRLDK
IQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMAN
LRKCGDNIKDFSKECRDALVKHTKWFSEEDEKINNACENESRILLEELNK
NVDNLKKKCA*
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Aliases
The feature 'SMED30002134' has the following synonyms
Synonym
NB.32.1g
prog-2
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0002032epidermal cell
PLANA:0002075pigment cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 138..158
NoneNo IPR availableTMHMMTMhelixcoord: 17..39