SMED30021080

Overview
NameSMED30021080
Smed IDSMED30021080
Length (bp)1020
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 SMED30021080 (SMED30021080) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021080 (SMED30021080) 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 SMED30021080 (SMED30021080) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021080 (SMED30021080) 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



SMED30021080

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30021080 Contig7687newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30021080 Contig7687uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
reproductive organSMED30021080 Contig18734uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30021080 Contig18734newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30021080 vs. TrEMBL
Match: A0A1X7V1Q7 (TTF-type domain-containing protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 1.731e-13
Identity = 30/69 (43.48%), Postives = 42/69 (60.87%), Query Frame = 1 
Query:  670 NIDIG-LLKLNLMRKDVEEAIQRGP*SHPATFPVDKQGNQFPVNLLKLRLKNNEIVARDWLAWSKSKNA 873
              DIG LLK  L   +V++ I  GP  +P +FP D +  +FPV++L  +L+N   V RDWL WS+ K A
Sbjct:  124 GCDIGKLLKTTLTDSEVKQTILSGPIHYPKSFPRDSKNVKFPVSILTSKLQNGNYVERDWLVWSEEKTA 192

HSP 2 Score: 43.1282 bits (100), Expect = 1.731e-13
Identity = 24/53 (45.28%), Postives = 33/53 (62.26%), Query Frame = 3 
Query:  864 EKCSVF-FPCRLFYNFREDQRSVLATELGWQPDRGYKKL*DRKPEHEKSTHHK 1019
            EK ++F FPCR+F      + S L++  GW  + G+KKL DR P HEKS  H+
Sbjct:  189 EKTALFCFPCRIF---SCSEVSHLSSVTGWSTEIGWKKLYDRIPMHEKSITHR 238
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BLAST of SMED30021080 vs. TrEMBL
Match: A0A2T7PZZ6 (Uncharacterized protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_01617 PE=4 SV=1)

HSP 1 Score: 72.7886 bits (177), Expect = 2.005e-11
Identity = 37/82 (45.12%), Postives = 51/82 (62.20%), Query Frame = 1 
Query:  628 EEASTSESMDVNLLN-IDIGLLKLNLMRK-DVEEAIQRGP*SHPATFPVDKQGNQFPVNLLKLRLKNNEIVARDWLAWSKSK 867
            EE+  +E+      N  ++GLL+        +EEAI+RGP + PA FP D  G  FPV+LL+++LKN E V RDWL WSK +
Sbjct:  103 EESLLTETTSTRPCNDFNVGLLETKTTSAYHIEEAIRRGPANLPACFPDDSSGRSFPVSLLQIKLKNGETVRRDWLVWSKER 184
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BLAST of SMED30021080 vs. TrEMBL
Match: A0A1X7SDC2 (DUF4371 domain-containing protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 8.152e-8
Identity = 30/68 (44.12%), Postives = 40/68 (58.82%), Query Frame = 1 
Query:  649 SMDVNLLNIDIGLLKLNLMRKDVEEAIQRGP*SHPAT-FPVDKQGNQFPVNLLKLRLKNNEIVARDWL 849
            S D+  +N D      ++  +DVE AI+ GP SH  T FP D +GN+FPVN+ K  LKN +   RD L
Sbjct:   31 SFDIGTINSD------HISPRDVENAIKFGPKSHVHTSFPRDCKGNRFPVNIFKHTLKNGDESTRDXL 92

HSP 2 Score: 33.8834 bits (76), Expect = 8.152e-8
Identity = 15/30 (50.00%), Postives = 19/30 (63.33%), Query Frame = 3 
Query:  930 LATELGWQPDRGYKKL*DRKPEHEKSTHHK 1019
            L +  GW  D G++KL DR PEHE S  H+
Sbjct:  105 LCSVDGWSVDMGWRKLYDRVPEHEHSIPHR 134
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BLAST of SMED30021080 vs. TrEMBL
Match: A0A1X7TU39 (Uncharacterized protein OS=Amphimedon queenslandica OX=400682 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 4.384e-6
Identity = 31/68 (45.59%), Postives = 41/68 (60.29%), Query Frame = 1 
Query:  649 SMDVNLLNIDIGLLKLNLMRKDVEEAIQRGP*SHPAT-FPVDKQGNQFPVNLLKLRLKNNEIVARDWL 849
            S D+  +N D      ++  +DVE AI+ GP SH  T FP D +GN+FPVN+ K  LKN +   RDWL
Sbjct:  128 SFDIGTINSD------HISPRDVENAIKFGPKSHVHTSFPRDCKGNRFPVNIFKHTLKNGDESTRDWL 189
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BLAST of SMED30021080 vs. Planmine SMEST
Match: SMESG000058689.1 (SMESG000058689.1)

HSP 1 Score: 106.686 bits (265), Expect = 6.929e-38
Identity = 63/69 (91.30%), Postives = 66/69 (95.65%), Query Frame = 2 
Query:  359 MSQHYKSGCXXXXXXXXXXXXNAIGRRTLENVGFITLSKSQQDEKQNPSESINAKESDGIPTLSLSTYV 565
            MSQ YKSGCEKR+ERQKKLE+NA GRR LEN+GFITLSKSQQDEKQNPSESINAKESDGIPTLSLSTYV
Sbjct:    1 MSQRYKSGCEKRKERQKKLEKNARGRRALENLGFITLSKSQQDEKQNPSESINAKESDGIPTLSLSTYV 69

HSP 2 Score: 69.707 bits (169), Expect = 6.929e-38
Identity = 34/37 (91.89%), Postives = 37/37 (100.00%), Query Frame = 1 
Query:  568 SSRTEETTFPLSEESANCKMEEASTSESMDVNLLNID 678
            SSRTEETTFPLSEESANC+M+EASTSESMD+NLLNID
Sbjct:   74 SSRTEETTFPLSEESANCEMKEASTSESMDLNLLNID 110
The following BLAST results are available for this feature:
BLAST of SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A1X7V1Q71.731e-1343.48TTF-type domain-containing protein OS=Amphimedon q... [more]
A0A2T7PZZ62.005e-1145.12Uncharacterized protein OS=Pomacea canaliculata OX... [more]
A0A1X7SDC28.152e-844.12DUF4371 domain-containing protein OS=Amphimedon qu... [more]
A0A1X7TU394.384e-645.59Uncharacterized protein OS=Amphimedon queenslandic... [more]
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BLAST of SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 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 SMED30021080 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000058689.16.929e-3891.30SMESG000058689.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021080 ID=SMED30021080|Name=SMED30021080|organism=Schmidtea mediterranea sexual|type=transcript|length=1020bp
CATCGTCGCACTTTGGGGGGATACGTCCCGCACAACTGGCCACGTAGTGG
TGTCCATAATGTCGATCGCGAAGCCTTTAAACTTTAAACCTTTAAATGAA
ATAAATATGATGGAAGAACAATAAGATTTTTTTTGTCTTTACATTTAGTC
GATCTTGGCAAGACATTTTTATAATCGATCTTCGAAAAGTCGATCGGTCA
AAAATTAGTGGACACCACTGATTTATATGATTGAAACGTGAAACGTATCG
ACCTTATTAGCAAAGCGATATTTTGCTTAATAACATGCAGCATCATTAAA
AAAAATAAATTAAATTTTAAAAAAATTAATAAATGATATTAATTTATGGA
CAGGGATAATGAGTCAGCATTATAAATCCGGATGCGAAAAGCGTAGAGAA
CGACAAAAGAAGCTTGAAGAAAATGCTATAGGAAGAAGAACATTAGAAAA
TGTGGGTTTCATAACTTTATCGAAATCCCAACAAGATGAAAAACAAAACC
CTTCCGAATCAATAAATGCAAAGGAATCTGACGGAATTCCTACACTTTCC
TTGTCTACGTATGTTCAAGTTCAAGAACCGAAGAAACAACATTTCCCTTG
TCTGAAGAATCGGCCAACTGTAAAATGGAAGAAGCATCCACCAGTGAATC
TATGGATGTGAATTTACTAAACATCGACATTGGATTGTTGAAATTAAATT
TAATGAGAAAGGATGTAGAAGAGGCTATTCAACGAGGTCCATAATCACAT
CCAGCAACATTTCCTGTTGATAAACAGGGCAATCAATTTCCAGTAAATTT
GTTAAAATTGCGTTTAAAAAATAATGAAATTGTTGCTCGAGATTGGCTTG
CTTGGAGCAAATCGAAAAATGCTCTGTTTTTTTTCCTTGTCGTTTATTTT
ATAATTTTCGAGAAGATCAAAGATCAGTTTTGGCTACGGAATTGGGTTGG
CAGCCTGATAGAGGATATAAAAAACTATAAGATAGAAAACCTGAGCATGA
AAAATCAACCCACCATAAAT
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protein sequence of SMED30021080-orf-1

>SMED30021080-orf-1 ID=SMED30021080-orf-1|Name=SMED30021080-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp
MSQHYKSGCEKRRERQKKLEENAIGRRTLENVGFITLSKSQQDEKQNPSE
SINAKESDGIPTLSLSTYVQVQEPKKQHFPCLKNRPTVKWKKHPPVNLWM
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0002089reproductive organ