SMED30021559

Overview
NameSMED30021559
Smed IDSMED30021559
Length (bp)1412
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 SMED30021559 (SMED30021559) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021559 (SMED30021559) 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 SMED30021559 (SMED30021559) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021559 (SMED30021559) 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.
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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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Homology
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BLAST of SMED30021559 vs. Planmine SMEST
Match: SMESG000029866.1 (SMESG000029866.1)

HSP 1 Score: 50.8322 bits (120), Expect = 1.197e-9
Identity = 23/42 (54.76%), Postives = 27/42 (64.29%), Query Frame = 1 
Query:   25 SRKICETCVHCPMIHENAK*GKLKTRLLTMMNENIQNKWQKD 150
            SR  C TC  C  IH  AK GKLKT+L+  M EN+ +KWQ D
Sbjct:  320 SRSDCVTCTQCQTIHTEAKIGKLKTKLIATMTENLFDKWQND 361

HSP 2 Score: 26.9498 bits (58), Expect = 1.197e-9
Identity = 15/50 (30.00%), Postives = 27/50 (54.00%), Query Frame = 2 
Query:  266 FNSFHNIIKHCQAGAKKTKIYA*NNFNMEDFEQLLFNTEQACENCQRGKS 415
            FN  +N++K  + G KK + Y  +N  M +    +    + CENC++ K+
Sbjct:  378 FNVENNLVKKIE-GIKKVEKYICHNIAMNNLSSKVKEVIEKCENCEKRKT 426

HSP 3 Score: 23.0978 bits (48), Expect = 1.197e-9
Identity = 8/26 (30.77%), Postives = 16/26 (61.54%), Query Frame = 3 
Query:  426 KTKEEIICSRESKLFSTNNVDLYNQR 503
            +TKE I+   + K+F    +D+Y ++
Sbjct:  430 RTKEPIVSQEDYKIFEVIYIDIYGKK 455
[Close]
BLAST of SMED30021559 vs. Planmine SMEST
Match: SMESG000029259.1 (SMESG000029259.1)

HSP 1 Score: 40.817 bits (94), Expect = 1.404e-9
Identity = 17/47 (36.17%), Postives = 32/47 (68.09%), Query Frame = 1 
Query:  493 TIRGERYIFGIINHHCKHISLHSVKTQNKKTVVRMLKEEGVMKY*AP 633
            T   ++YI GII+H+ K+ISL ++  Q+++T+   L  + ++K+ AP
Sbjct: 3307 TFNKKKYICGIIDHYSKYISLTAINKQDERTISETLLNKWILKFGAP 3353

HSP 2 Score: 31.9574 bits (71), Expect = 1.404e-9
Identity = 20/48 (41.67%), Postives = 26/48 (54.17%), Query Frame = 2 
Query:  716 ILSKP----VNGQIERQFRKIRDAIQITL*DKPHKSWVHF--HIEYSL 841
            I S P     NG IERQFR IR+ I  +L +   K+W      I+Y+L
Sbjct: 3381 IFSSPYHHNTNGIIERQFRTIREYINASLNEGGRKNWADIVPEIKYTL 3428

HSP 3 Score: 27.7202 bits (60), Expect = 1.404e-9
Identity = 14/36 (38.89%), Postives = 19/36 (52.78%), Query Frame = 2 
Query:  296 CQAGAKKTKIYA*NNFNMEDFEQLLFNTEQACENCQ 403
            C AGA+K   Y  NN +ME+    +    + CE CQ
Sbjct: 3236 CHAGAQKVTKYIQNNCDMENLATEVKKVIENCERCQ 3271

HSP 4 Score: 56.6102 bits (135), Expect = 4.395e-8
Identity = 27/49 (55.10%), Postives = 34/49 (69.39%), Query Frame = 1 
Query:   25 SRKICETCVHCPMIHENAK*GKLKTRLLTMMNENIQNKWQKDSSVVERL 171
            SRK C TCV C M HE+AK GK+KTR+LT+  E   NKWQ D+  V+ +
Sbjct: 3144 SRKTCGTCVQCMMEHEDAKTGKIKTRILTVTAEGGYNKWQNDNMEVQEI 3192
The following BLAST results are available for this feature:
BLAST of SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 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 SMED30021559 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000029866.11.197e-954.76SMESG000029866.1[more]
SMESG000029259.11.404e-936.17SMESG000029259.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021559 ID=SMED30021559|Name=SMED30021559|organism=Schmidtea mediterranea sexual|type=transcript|length=1412bp
GCAGTACAGAAAAAAAAATCTTAGTCAAGAAAGATATGCGAAACTTGTGT
GCATTGTCCAATGATTCATGAAAATGCTAAATGAGGTAAATTAAAAACAA
GATTGTTAACAATGATGAATGAAAATATACAAAATAAATGGCAAAAGGAT
TCCAGTGTAGTTGAAAGATTATAAAAAGTGACCCAAATAAAACATCTTTT
AAATGTATAAATAAAGTCATATTGACAGATAATAATAAAATTTTGGATTT
CAGATGAAAATAAATTTTAATTCATTTCATAACATCATAAAACACTGCCA
GGCTGGTGCTAAGAAAACTAAAATTTATGCTTAAAATAATTTTAACATGG
AAGATTTCGAACAATTGCTTTTTAATACTGAACAAGCTTGTGAAAACTGT
CAGAGGGGAAAAAGCTGATATAACTAAAACTAAAGAAGAAATAATATGTT
CAAGGGAATCTAAGTTATTTTCAACAAACAATGTGGACCTTTACAATCAG
AGGTGAACGATATATCTTTGGAATTATAAATCATCATTGTAAACATATTT
CCCTCCATTCAGTTAAAACACAGAATAAAAAGACAGTGGTTCGAATGCTT
AAAGAAGAGGGGGTAATGAAATATTGAGCGCCGAGTATAATTAATTGTGA
GAGGAGAAAGTCATTCAAATCCAAATCATCAAGCATATTTGCTGAAAAAA
CAATATTGAAATACAATATTATCCAAGCCCGTGAATGGGCAGATTGAGAG
ACAATTTAGAAAGATTAGAGATGCAATCCAGATAACACTTTAGGATAAGC
CGCATAAATCTTGGGTTCACTTTCACATTGAATACAGTTTATGGTTAGTT
TAACTNNNNNNNNNNTTAGTTTAACTTTCAAAAAACTAATAAAAAGCCTT
CTAGTGGAATGGCTTTTGGATAAAAGAACTTATAGTTTTCAGAAGCATCT
TTGTGGAAGAAGTCTATCGAAAGCGGAATCGTGAATTTAAAATTATATAT
TGGACCAGGAGAGGTGGAAGCTGTGAAATAAAAAGGACAAATGGAAATAA
CTTAATCAGAAACGTCTTAATCAGAAACGTCGAATGGCTAAAGGAGATAG
GCCAAGCTGCATTGTACAATCTGTCCTCGATCTATTTAAACTTGGAATGT
ATTAATTACAGAAAATTAATTTGTAAAAGTATAAAAATCAGTTAAATAGA
AATTCCTGCAGGAGTCCATCTTTTACAGATTCGCCAACAATCCTACTAAA
AGATCGGAGAGATGAGCTAAACAGAAAAGACAATTAAATATGAAATACTG
GATAATGCTATAACATAAGAAGTGCAAGTAAGAGAAGCGACCAATGGTGC
AGAAGAGCAAATATTCAATATCATTTTTATTACAATACTTATAATTTAAT
TAATCGTCTTTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000101muscle cell
PLANA:0000421tail
PLANA:0003116parenchymal cell
PLANA:0003117parapharyngeal cell