X1.A5.1

Overview
NameX1.A5.1
Smed IDSMED30002753
Length (bp)514
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.A5.1 (SMED30002753) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.A5.1 (SMED30002753) 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.A5.1 (SMED30002753) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.A5.1 (SMED30002753) 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




SMED30002753

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle progenitor cellSMED30002753SMESG000062836.1 SMED30002753smed_20140614PMID:29906446
Zeng et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30002753SMESG000062836.1 dd_Smed_v4_585_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002753SMESG000062836.1 Contig42508newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30002753SMESG000062836.1 Contig42508uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30002753SMESG000062836.1 dd_Smed_v6_585_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
neuronSMED30002753SMESG000062836.1 Contig42508newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30002753SMESG000062836.1 Contig42508uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016
whole organism asexual adult colorimetric in situ hybridization evidence
glial cellSMED30002753SMESG000062836.1 dd_Smed_v6_585_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of X1.A5.1 vs. TrEMBL
Match: V9XRK5 (X1.A5.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 186.808 bits (473), Expect = 2.990e-58
Identity = 86/87 (98.85%), Postives = 87/87 (100.00%), Query Frame = 3
Query:  174 TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSF+NDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR
Sbjct:   21 TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSFHNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 107          
BLAST of X1.A5.1 vs. TrEMBL
Match: A0A1S8X0S1 (Uncharacterized protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=X801_03822 PE=4 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 1.568e-6
Identity = 25/70 (35.71%), Postives = 36/70 (51.43%), Query Frame = 3
Query:  225 YRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            YRF+  TG F C   +   CF++C + GC+EW F N I   +      H CRC+ +L  C +  +P   R
Sbjct:   12 YRFDPKTGTFLCVVPTAKLCFELCQSIGCNEWFFANMISTRNETVLPYHRCRCVPQLRMCLYNPVPRAYR 81          
BLAST of X1.A5.1 vs. TrEMBL
Match: A0A4S2LQR5 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_005512 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 2.455e-6
Identity = 25/70 (35.71%), Postives = 36/70 (51.43%), Query Frame = 3
Query:  225 YRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            YRF+  TG F C   +   CF++C + GC+EW F N I   +      H CRC+ +L  C +  +P   R
Sbjct:   50 YRFDPKTGTFLCVVPTAKLCFELCQSIGCNEWFFANMISTRNETVLPYHRCRCVPQLRMCLYNPVPRAYR 119          
BLAST of X1.A5.1 vs. TrEMBL
Match: G7YMD2 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_112195 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 2.785e-6
Identity = 25/70 (35.71%), Postives = 36/70 (51.43%), Query Frame = 3
Query:  225 YRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            YRF+  TG F C   +   CF++C + GC+EW F N I   +      H CRC+ +L  C +  +P   R
Sbjct:   47 YRFDPKTGTFLCVVPTAKLCFELCQSIGCNEWFFANMISTRNETVLPYHRCRCVPQLRMCLYNPVPRAYR 116          
BLAST of X1.A5.1 vs. TrEMBL
Match: A0A074ZEM9 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=T265_06924 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 3.688e-6
Identity = 25/70 (35.71%), Postives = 36/70 (51.43%), Query Frame = 3
Query:  225 YRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            YRF+  TG F C   +   CF++C + GC+EW F N I   +      H CRC+ +L  C +  +P   R
Sbjct:   41 YRFDPKTGTFLCVVPTAKLCFELCQSIGCNEWFFANMISTRNETVLPYHRCRCVPQLRMCLYNPVPRAYR 110          
BLAST of X1.A5.1 vs. Planmine SMEST
Match: SMESG000062836.1 (SMESG000062836.1)

HSP 1 Score: 191.815 bits (486), Expect = 1.193e-60
Identity = 86/87 (98.85%), Postives = 87/87 (100.00%), Query Frame = 3
Query:  174 TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 434
            TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSF+NDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR
Sbjct:  249 TEEEHTDFGYKCNARNKYRFNATTGLFHCTTISPADCFKMCVATGCHEWSFHNDIDGFDPNPFYTHFCRCIRRLDSCYFGLIPWEMR 335          
The following BLAST results are available for this feature:
BLAST of X1.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
V9XRK52.990e-5898.85X1.A5.1 (Fragment) OS=Schmidtea mediterranea OX=79... [more]
A0A1S8X0S11.568e-635.71Uncharacterized protein (Fragment) OS=Opisthorchis... [more]
A0A4S2LQR52.455e-635.71Uncharacterized protein OS=Opisthorchis felineus O... [more]
G7YMD22.785e-635.71Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A074ZEM93.688e-635.71Uncharacterized protein OS=Opisthorchis viverrini ... [more]
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BLAST of X1.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 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.A5.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000062836.11.193e-6098.85SMESG000062836.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002753 ID=SMED30002753|Name=X1.A5.1|organism=Schmidtea mediterranea sexual|type=transcript|length=514bp
TAGCAATGTGATTAGCAGCGTGTATGGCTTCAATAAAATCTGAATCGTGA
TTGGCTGAAAAAAGGATTTAAATGAAATCATTACACAGCCCACAATTCGC
CAGCGCGTTAATTATGATTCAGCAGATATTACAGTTAATTTTCATCAGTT
TTCTATTTGGTTTTCTCCAAAGTACAGAAGAAGAGCACACTGACTTTGGG
TACAAGTGCAATGCCCGTAACAAGTACAGATTCAATGCTACCACCGGATT
GTTCCATTGTACAACAATCAGTCCAGCCGATTGTTTCAAAATGTGTGTTG
CCACTGGTTGCCACGAATGGTCATTTTACAATGATATTGATGGATTTGAC
CCGAATCCTTTTTATACTCACTTTTGCCGATGCATCAGAAGGTTAGACAG
CTGCTATTTTGGTTTGATACCGTGGGAAATGAGGTTGAATGGATTTTTAA
ATGATTAAATCAATCTTATTTAATTGTTAATAAATTTCTTAATAAAATTT
GTTTTAGATTTTTT
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protein sequence of SMED30002753-orf-1

>SMED30002753-orf-1 ID=SMED30002753-orf-1|Name=SMED30002753-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=129bp
MKSLHSPQFASALIMIQQILQLIFISFLFGFLQSTEEEHTDFGYKCNARN
KYRFNATTGLFHCTTISPADCFKMCVATGCHEWSFYNDIDGFDPNPFYTH
FCRCIRRLDSCYFGLIPWEMRLNGFLND*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000019muscle progenitor cell
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000418head
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 10..32