X1.C.A4.1

Overview
NameX1.C.A4.1
Smed IDSMED30035648
Length (bp)414
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 X1.C.A4.1 (SMED30035648) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.C.A4.1 (SMED30035648) 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 X1.C.A4.1 (SMED30035648) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.C.A4.1 (SMED30035648) 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



SMED30035648

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30035648SMESG000028445.1 dd_Smed_v4_3815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30035648SMESG000028445.1 dd_Smed_v4_3815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30035648SMESG000028445.1 dd_Smed_v4_3815_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035648SMESG000028445.1 Contig2997newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035648SMESG000028445.1 Contig2997uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035648SMESG000042355.1 Contig2997newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30035648SMESG000042355.1 Contig2997uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30035648SMESG000028445.1 dd_Smed_v4_3815_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30035648SMESG000028445.1 dd_Smed_v4_3815_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
Homology
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BLAST of X1.C.A4.1 vs. TrEMBL
Match: V9XRN7 (X1.C.A4.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 151.754 bits (382), Expect = 3.069e-45
Identity = 83/83 (100.00%), Postives = 83/83 (100.00%), Query Frame = 1 
Query:   43 MSHXXXXXXXXXXTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGG 291
            MSHFVSIFISIIVTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGG
Sbjct:    1 MSHFVSIFISIIVTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGG 83
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BLAST of X1.C.A4.1 vs. Planmine SMEST
Match: SMESG000028445.1 (SMESG000028445.1)

HSP 1 Score: 155.992 bits (393), Expect = 1.492e-50
Identity = 85/85 (100.00%), Postives = 85/85 (100.00%), Query Frame = 1 
Query:   43 MSHXXXXXXXXXXTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGGYF 297
            MSHFVSIFISIIVTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGGYF
Sbjct:    1 MSHFVSIFISIIVTSLFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGGYF 85
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BLAST of X1.C.A4.1 vs. Planmine SMEST
Match: SMESG000032824.1 (SMESG000032824.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.686e-11
Identity = 26/70 (37.14%), Postives = 40/70 (57.14%), Query Frame = 1 
Query:   88 LFDYSTSIPACGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGGYF 297
            LF    S   CG NP+ I +  + S  GGK + D+ALE++K+ +   YN+L      W+ CN+R + GY+
Sbjct:   15 LFLELVSANICGNNPVEIIDYLIRSESGGKATVDEALEFIKIHDSKFYNKLLSDVKLWLECNQRYDTGYY 84
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BLAST of X1.C.A4.1 vs. Planmine SMEST
Match: SMESG000050337.1 (SMESG000050337.1)

HSP 1 Score: 42.3578 bits (98), Expect = 5.754e-6
Identity = 24/75 (32.00%), Postives = 34/75 (45.33%), Query Frame = 1 
Query:   85 SLFDYSTSIPA----CGINPLRIFENEVLSRGGGKVSFDQALEYLKVQNPSSYNELNQITMRWILCNRRSEGGYF 297
            S+   +TSI      CG NPL + +N         VS    L     +NP++Y  L      W +C R+S+ GYF
Sbjct:    8 SMLILTTSIIVNGNGCGTNPLAVIQNMYEKGKEMPVSLKYVLRNFAAKNPTAYRSLMDHYQTWQMCIRKSDIGYF 82
The following BLAST results are available for this feature:
BLAST of X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRN73.069e-45100.00X1.C.A4.1 (Fragment) OS=Schmidtea mediterranea OX=... [more]
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BLAST of X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 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 X1.C.A4.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000028445.11.492e-50100.00SMESG000028445.1[more]
SMESG000032824.11.686e-1137.14SMESG000032824.1[more]
SMESG000050337.15.754e-632.00SMESG000050337.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30035648 ID=SMED30035648|Name=X1.C.A4.1|organism=Schmidtea mediterranea sexual|type=transcript|length=414bp
AGAGTAGGTTTTTTTCTATTGATATTCATCTAAAATCATACAATGAGCCA
TTTTGTGAGCATTTTTATTTCTATCATAGTGACATCTCTATTCGACTATT
CAACGAGTATTCCTGCCTGTGGGATAAATCCTTTAAGGATATTTGAAAAT
GAAGTCCTTAGTAGAGGAGGCGGAAAAGTCTCATTTGACCAAGCCTTGGA
ATATTTGAAGGTTCAAAATCCAAGTTCATACAATGAGTTAAATCAAATCA
CAATGCGATGGATTCTATGCAACAGAAGGTCAGAGGGAGGATATTTCTAA
AAAAATGAAGGAAATGGTTTCAAGTTGAATTTTTCATCAATTTTCTACTT
TATTGAATTGCCATTTCATTTATGAGAGTGATAAAAGTAATAAATAAATT
TATTATTGGTTTTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000028Category 2 cell
PLANA:0000240body wall musculature
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..22
score: 0.598