SMED30024126

Overview
NameSMED30024126
Smed IDSMED30024126
Length (bp)626
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30024126 (SMED30024126) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024126 (SMED30024126) in cells (dots) of each of the 12 neoblast clusters.

 

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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




SMED30024126

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



PAGE Curations: 27

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30024126h1SMcG0017355 SmedASXL_008636SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30024126h1SMcG0017355 SmedASXL_008636SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30024126h1SMcG0017355 SmedASXL_012769SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30024126h1SMcG0017355 SmedASXL_012769SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30024126h1SMcG0017355 SmedASXL_009917SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30024126h1SMcG0017355 SmedASXL_009917SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30024126h1SMcG0017355 SmedASXL_012768SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30024126h1SMcG0017355 SmedASXL_012768SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30024126h1SMcG0017355 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30024126h1SMcG0017355 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024126h1SMcG0017355 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024126h1SMcG0017355 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024126h1SMcG0017355 Contig45411newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024126h1SMcG0017355 Contig45411uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
cephalic gangliaSMED30024126h1SMcG0017355 dd_Smed_v4_4504_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30024126h1SMcG0017355 dd_Smed_v4_4504_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024126h1SMcG0017355 dd_Smed_v4_4504_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024126h1SMcG0017355 dd_Smed_v4_4504_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024126h1SMcG0017355 SMED_02039_V2_1rGPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_02039_V2_1rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_01263_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_01263_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SmWIOct06_043235GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SmWIOct06_035939GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_37391_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_02039_V2_2rGPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30024126h1SMcG0017355 SMED_02039_V2_2rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024126 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001069:25076..25802 +3074
Homology
BLAST of SMED30024126 vs. Planmine SMEST
Match: SMESG000053935.1 (SMESG000053935.1)

HSP 1 Score: 135.576 bits (340), Expect = 1.004e-36
Identity = 73/73 (100.00%), Postives = 73/73 (100.00%), Query Frame = 1
Query:   97 AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK 315
            AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK
Sbjct:   21 AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK 93          
The following BLAST results are available for this feature:
BLAST of SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 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 SMED30024126 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000053935.11.004e-36100.00SMESG000053935.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024126 ID=SMED30024126|Name=SMED30024126|organism=Schmidtea mediterranea sexual|type=transcript|length=626bp
GTTTTAAATACATTTAAAAAGTAACGCATCGTGAAAATGTCTAAAAGCAA
AAATCAAAAGAAATCTAATAATAAGCCTTCAAATGTTCCGGTGAAAGCTC
AAAATTTAAAACCTAATAAAAATGGACAAAAAATTAACAATAATCCAGCA
CTCAACAAAAAACAAATTATCAACTCAACTGATAAGGTCAACCAAAAACC
AGTAACTAATTCTATTGCCAAAGTTCAGCCAATCAAAACTGAATTGTCCA
AGAATGAAAGCAATGCAATTAAAAAGTCTGTTGTTGAAAAGAAAAATGTG
AAACTTCTCCAAAAAGAAATAGATATTGCTGAATCTGGTGAAGATGAAGA
CGAAGATGATATTGAATTTGAGGATGATTCTGATATTGACGATGTCGATC
TTGGCGATTCAGATGATGATCTCGATCTTGGAGATTCAGATGATGATCTT
GGAGATTCAGATGATGATTTATCAGTTATGGACTTGAATTCTGATTTAGA
AAGCATCGAGTTAGATGAAGATGCTATTGATGAAGCCGAAGTTGAAATTA
AGAAAAAACCAATAAAGAAGGAATCTTCTAAGCCAGCTGAGAAGAAGGAA
GTTCCTAAACCAGCTGAGAAGAAGGA
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protein sequence of SMED30024126-orf-1

>SMED30024126-orf-1 ID=SMED30024126-orf-1|Name=SMED30024126-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=196bp
MSKSKNQKKSNNKPSNVPVKAQNLKPNKNGQKINNNPALNKKQIINSTDK
VNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQKEIDIAES
GEDEDEDDIEFEDDSDIDDVDLGDSDDDLDLGDSDDDLGDSDDDLSVMDL
NSDLESIELDEDAIDEAEVEIKKKPIKKESSKPAEKKEVPKPAEKK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..61
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 169..196
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 96..145
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 98..145
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 7..61