SMED30028506

Overview
NameSMED30028506
Smed IDSMED30028506
Length (bp)1340
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 SMED30028506 (SMED30028506) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028506 (SMED30028506) 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 SMED30028506 (SMED30028506) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028506 (SMED30028506) 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



SMED30028506

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30028506 dd_Smed_v4_20920_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30028506 dd_Smed_v4_20920_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
SMED30028506 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.023049:1936..3412 +6480
v31.011262:9729..11205 -6453
Homology
[Close]
BLAST of SMED30028506 vs. Planmine SMEST
Match: SMESG000033008.1 (SMESG000033008.1)

HSP 1 Score: 100.138 bits (248), Expect = 1.893e-24
Identity = 52/101 (51.49%), Postives = 72/101 (71.29%), Query Frame = -1 
Query:  675 RLPKISKIVAALLSPPATHPQSPLETRHKEF---RAKYEKLKRTWSSPEKTHGLHQKITRVSRARDDLIIENLSQRITIAEHSAALH*IFTKKELPARLSA 968
            R+P++S ++ A+           LET  ++F   ++KY+K+K TWS PE T  L+QK++R+SRARDDL++EN SQRITIAE SAAL  IFT+ EL ARLS+
Sbjct:    9 RIPRLSPLITAMFQR--------LETLERDFTALKSKYQKIKGTWSPPEATRNLYQKLSRLSRARDDLVVENRSQRITIAEQSAALRQIFTENELRARLSS 101
[Close]
BLAST of SMED30028506 vs. Planmine SMEST
Match: SMESG000011251.1 (SMESG000011251.1)

HSP 1 Score: 97.8265 bits (242), Expect = 3.608e-23
Identity = 61/116 (52.59%), Postives = 74/116 (63.79%), Query Frame = -1 
Query:  633 MRLPKISKIVAALLSPPATHPQSPLETRHKE---FRAKYEKLKRTWSSPEKTHGLHQKITRVSRARDDLIIENLSQRITIAEHSAALH*IFTKKELPARLSAGARPSRLILFQLTI 971
            M +P+I +IV   L+P A      LE   +E      KYEK+K TW SPE T  L++KITR+SRARDDLIIE  SQRITI+E +AAL  IFT KEL ARL     PSR +  Q+ I
Sbjct:    1 MTMPRIPRIV---LAPSAVAMNQRLENLERENLILGEKYEKIKGTWCSPEATKELYKKITRLSRARDDLIIETRSQRITISEKNAALRQIFTVKELQARL-----PSRTLAQQINI 108
[Close]
BLAST of SMED30028506 vs. Planmine SMEST
Match: SMESG000069750.1 (SMESG000069750.1)

HSP 1 Score: 98.9821 bits (245), Expect = 4.147e-23
Identity = 56/100 (56.00%), Postives = 68/100 (68.00%), Query Frame = -1 
Query:  675 LPKISKIVAALLSPPATHPQSPLETRHKEFRA---KYEKLKRTWSSPEKTHGLHQKITRVSRARDDLIIENLSQRITIAEHSAALH*IFTKKELPARLSA 965
            LP+I +     LSP  T     LE+  +EF     KY+++K TWSSPE T GL QKITR++RARDDLIIEN  QR+TIAE S AL  IFT+ EL ARLS+
Sbjct:    7 LPRIPR-----LSPSVTAVSQRLESLEREFATLWEKYQRVKSTWSSPETTKGLFQKITRLTRARDDLIIENRGQRLTIAEQSVALRKIFTENELRARLSS 101
[Close]
BLAST of SMED30028506 vs. Planmine SMEST
Match: SMESG000055478.1 (SMESG000055478.1)

HSP 1 Score: 98.2117 bits (243), Expect = 4.487e-23
Identity = 60/116 (51.72%), Postives = 73/116 (62.93%), Query Frame = -1 
Query:  624 MRLPKISKIVAALLSPPATHPQSPLETRHKEFRAKYEKLKRTWSSPEKTHGLHQKITRVSRARDDLIIENLSQRITIAEHSAALH*IFTKKELPARLSAGARPSRLILFQLTIYQG 971
            M LP I +IV A  +   T     L+  +   R KYEKLK TW SPE T   ++KITR+SRARDDLIIE  SQRITI+E +AA   IFT+KEL ARL     PSR ++ Q+ I Q 
Sbjct:    1 MNLPSIPRIVLAPSAVAMTQRLEKLKWENFVLREKYEKLKGTWCSPEATKEQYKKITRLSRARDDLIIETRSQRITISEQTAAFRQIFTEKELQARL-----PSRNLVQQINIIQA 111
[Close]
BLAST of SMED30028506 vs. Planmine SMEST
Match: SMESG000011251.1 (SMESG000011251.1)

HSP 1 Score: 96.2857 bits (238), Expect = 1.298e-22
Identity = 60/114 (52.63%), Postives = 73/114 (64.04%), Query Frame = -1 
Query:  633 LPKISKIVAALLSPPATHPQSPLETRHKE---FRAKYEKLKRTWSSPEKTHGLHQKITRVSRARDDLIIENLSQRITIAEHSAALH*IFTKKELPARLSAGARPSRLILFQLTI 965
            +P+I +IV   L+P A      LE   +E      KYEK+K TW SPE T  L++KITR+SRARDDLIIE  SQRITI+E +AAL  IFT KEL ARL     PSR +  Q+ I
Sbjct:    1 MPRIPRIV---LAPSAVAMNQRLENLERENLILGEKYEKIKGTWCSPEATKELYKKITRLSRARDDLIIETRSQRITISEKNAALRQIFTVKELQARL-----PSRTLAQQINI 106
The following BLAST results are available for this feature:
BLAST of SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 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 SMED30028506 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033008.11.893e-2451.49SMESG000033008.1[more]
SMESG000011251.13.608e-2352.59SMESG000011251.1[more]
SMESG000069750.14.147e-2356.00SMESG000069750.1[more]
SMESG000055478.14.487e-2351.72SMESG000055478.1[more]
SMESG000011251.11.298e-2252.63SMESG000011251.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028506 ID=SMED30028506|Name=SMED30028506|organism=Schmidtea mediterranea sexual|type=transcript|length=1340bp
TTTTTAAACCCTAACTATTTTTATTTCTAAAGTTACATTTATTTATGTCA
AACAACAACAACACAAAAGAATGAAGTTCTCATTCATCGTCAGCATCGAT
ATCGACGGGGAAATAACGCTTCGTCTGTTTTCGTTGGGCTAAAAAGATAT
CTTCTCGAGACACTCTCCCAGAAATCAAATTTATATACGGAACATCCTGA
GGGATCTCTGGTTCGAATATAACGAGAGGTGTCGAACCAGCACTCGTGAC
AAGAGAACTATCGGTCCAGCACTGATGGTCAATTTCAAGTTCTATGGAAT
CCTGACATTGAAATTTTCTATACTCATTTTCGCCTGATTCGAATCCAGTG
GAGAGAGACTACCAATGTGAGGGTGCATAGACAACTTCCAGATCTCGATC
CACTTTTTGCAGAAGCGAGTAGAGCAGTTTGAGTTCCAGAGAGTTGTAAG
TGTCATACTGGAGGTTGCTGTTTCGGAAGCTCGTAGGACATTCTCAACCT
GGCATTTTTCTCGTCGCCTTCGATTTTTGTTCGCCTTATGCCTTGAGTGA
TGGGCAGAAATGTGAGATATTTTCCTTGTCGTAGTTAAACTTATGTTTCC
CTGACCCGCTGGATTGGTCGACAACCCTGGTAAATGGTAAGCTGGAATAA
TATTAATCTGCTGGGCCGTGCTCCTGCCGACAGACGCGCCGGCAACTCCT
TTTTGGTGAAGATCTAGTGGAGTGCAGCGCTATGCTCCGCGATCGTGATT
CGCTGTGAGAGATTTTCAATGATCAGGTCATCTCTGGCGCGCGAAACTCG
CGTGATCTTCTGGTGCAATCCATGAGTCTTCTCTGGAGAGGACCACGTCC
TCTTTAATTTCTCATATTTGGCTCGGAACTCTTTATGTCTAGTCTCTAAA
GGGGATTGAGGATGTGTGGCCGGCGGAGATAACAGAGCCGCAACGATTTT
TGAGATTTTAGGAAGCCTCATTTTCAGAATGTTATTCACAATTTCGCGAT
CTCACACAGTTTAAATTTTGTTCTGTACTTTTGACAAATATTATTTGAAC
AGGTAAGCAAGTTTTATACTCATGTTATCAAATTTCGCATCTCGCCCACC
CGATCCGCCTACACTCTACGAAGTCGAAGCTCAATGGATTTGAATACTAC
GCTAATCGATGTATGGTGACGATTATAGTTTAAAAATGATTTTTTGTGAT
TATATCTCAGTGGATACTGTGGATCAAAGTGCAATTAAGGTTCTTGAAAC
TTATACTGTATCGCCATTTCTCATTTAAATCGAATTTAAGTTTATTTACC
GCTATTTAATTATATGGTATGACTTTTTATATGATTGTTG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell