SMED30017824

Overview
NameSMED30017824
Smed IDSMED30017824
Length (bp)3560
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30017824 (SMED30017824) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017824 (SMED30017824) in cells (dots) of each of the 12 neoblast clusters.

 

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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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Anatomical Expression

PAGE et. al., 2020



SMED30017824

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30017824 SmedASXL_032786SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30017824SMESG000029435.1 dd_Smed_v4_8467_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30017824SMESG000029435.1 dd_Smed_v4_8467_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017824SMESG000029435.1 dd_Smed_v4_8467_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30017824SMESG000029435.1 dd_Smed_v4_8467_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30017824SMESG000029435.1 dd_Smed_v4_8467_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017824 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000415:143012..148773 -17728
Homology
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BLAST of SMED30017824 vs. Planmine SMEST
Match: SMESG000029435.1 (SMESG000029435.1)

HSP 1 Score: 204.527 bits (519), Expect = 5.388e-53
Identity = 97/102 (95.10%), Postives = 100/102 (98.04%), Query Frame = 1 
Query: 2242 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQVCFNSIK 2547
            KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQ  F+S++
Sbjct:  988 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQFTFDSLE 1089
[Close]
BLAST of SMED30017824 vs. Planmine SMEST
Match: SMESG000029435.1 (SMESG000029435.1)

HSP 1 Score: 204.527 bits (519), Expect = 5.494e-53
Identity = 97/102 (95.10%), Postives = 100/102 (98.04%), Query Frame = 1 
Query: 2242 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQVCFNSIK 2547
            KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQ  F+S++
Sbjct:  979 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQSACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIEKYPRQFTFDSLE 1080
[Close]
BLAST of SMED30017824 vs. Planmine SMEST
Match: SMESG000029435.1 (SMESG000029435.1)

HSP 1 Score: 72.0182 bits (175), Expect = 3.086e-12
Identity = 35/35 (100.00%), Postives = 35/35 (100.00%), Query Frame = 1 
Query: 2242 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMK 2346
            KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMK
Sbjct:  988 KPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMK 1022
The following BLAST results are available for this feature:
BLAST of SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 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 SMED30017824 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000029435.15.388e-5395.10SMESG000029435.1[more]
SMESG000029435.15.494e-5395.10SMESG000029435.1[more]
SMESG000029435.13.086e-12100.00SMESG000029435.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017824 ID=SMED30017824|Name=SMED30017824|organism=Schmidtea mediterranea sexual|type=transcript|length=3560bp
CCCAATTCTAAGGTTTGTATATCATAATATTACTTTTATTATTATTGAAT
CTCTTGGAAATTTACTGAGTTATTAATTTACCTCATAAATTCAAATAAAC
TTTGCTATTTCTTTAAGAATGTGATGTGATTTAGGAGTCACTTTTAGAAA
AATTTTCGCCATTTACCTCACGTAATTGTTTAATGTCAGAATAGCGGCCT
TTCTTTATCGGAAATAATAAAGTAAAATATGGTCCAAATTTTTATTTTCT
GTTTTAAATCTGCTCTAAAAAAAGCGATTATTAAAACCTTTACATTTGCA
TGTTCTAAAATGTCATTGGATAAGTGTTATTATTATTCATTTGCGGTTTA
AAAGAAAGTCAATCAAAAATTTCAATGGCTAATTGGCCAACCCAATGCAG
GTAGACTTTGTGGAATATATGGATATGTTTCCACTTGTCTTAACTCTAAT
AGTTATTATTTTGAATTAATCGAGTTTCATGAAAGAAAGGCATCATTTGG
GTTGTTGTCAAAAATTATATTTAGGAAAATTGTTATTTATTTTTTGCGTC
CCAAGAAAATATAATGGCTATTAAATTTGAGGTTATGAATAATGTAATCA
TTGACCAAAAGCACCTGTATCAATACTCTATATACGAGGTCTTACAGATT
TGTATAAATTTGGAAAACTATAGATTAATGACTACTATTATTGCCTATAT
GCTGATTAAAATGGGGTTTCCGTTTCTGGGAACATGCATGGAAATTATTT
TCTCTAATACTAAATATTAGTTGTATTACATGTTTTTGGATATGATTTAT
ACTAAAAATAGCTCAAATTTGTGGAAATAATTAGAAATCACGGAGAGCTG
AGTCAAGTGAACAGTGGTAACATCACCCGACGCTCGTTTTGTTTATACGT
CAAGATCCTAGGCCCGATTTTTTCAAATTGTTTCTCGATTAATCTGGAAT
TTTTCAGTTATTTAAGTCATATCGGCTGTTGAACCATATTACATTTCGTA
CAATCCGCTTTTAAGGTCATCCACTATATATTCTCGTAAATCTTCTATTC
CACTGAACAGACTCGACTTCATATCTTCACCATATACGATTTGCAACAGC
TAAAACTCATTTACCTCAATAACTCGAATACTCATGTGATTTCGATGCAA
TAACGTCATAGTTGACACTTAACTTTAATTATATTCTGATTGTTTACATT
ATATATCTATTATATGATGATATAATGAATTAAAAGAATAAAATAATTCT
TGATACAACAAAGCAGAATAATTATGAAGACTCACGTAAATCCCAGGTTG
CATATGAGTCTGATATGCCATTATGTGCAAAAAACATCTGCAGGCTTTAA
TCTTCTGGAGAATTGATTGAACAAATCGTCCTAATAAATTTAGTAGTGCT
CGTGCCAACTCGGGAACGTCGGCGGTTAAAATTTAAATATCCTTTCCTAC
TACCTTACTGGTTATTATCCATAATTCCATTTCAATGTGGTCACGGCACT
ATGGACTCCAGCTCAGGATAATGATGTATACCCCAGCAGGAATATTCTAT
TACCGTATATGCATTGCAATATGCATGTTGATTTCCAAAATTTCTATTCT
AAATTTCCTATAAGTTATTAAAATACATATATTATATCGAAGTAGCAAAA
CCCACAGGGTTATGAGTCCATTTAATTTTTGTCAAGCATTGAGAATTATG
TAATCTGGTACTTTATTTTCATGTAACGTTGTGCCATTGTGGGAATCGCT
TAATGATCACATTGTCTACTACTTTCTCCCATTTCATATATCCTTACAAT
GAATAAAATATGTGGCTCTAAACGTGCGACTAAAACTTCATTTAATAAAA
TGATCTTTTATTCAATTCAAGAAAAACGCATTTGATACAAGTTGGATAAT
TTTCCATATTTCCTATGTTGCATGAATATTTCCCAGGGATTCGTCTGGCA
CAATTTAGGGAATGCGTATAGCACTATTTTCTAGTAGCATGTCACGGTGG
CTCATGACATTTTTGAGTCCTATTCAGGAAAAATAAATTCCCCATTCAAC
TTATATCTTCACACGTTATTGCTATTTATTATTTTAATTTAATTTTCTAC
AACGTTTCGAGTACACTAGTCAATTGTTTCCAGGATTTCTTGTGATGTTT
CGATGTGGGCTAGAAGCTCTTTTGATTGTTTTAGACAAATAAATTTCAAT
TGTTTTACTAAATGATTTCCATTTACTACATTTACTGTTTAAAGCCGAAA
ATGTCGATGCCCGTCATTGATAATTCATCAAATTTGATGAACAATCCCAG
CATGGTGAAAGTGAAATCCGTCAGCGGTAATCTATTAGAAATGAAAAAAT
CAGCCATTCAATCGGCATGCATAGTCACGAATGCAAACCCAATGTCTCCG
AGTAGACCAGCGGTTCACCATCGGCATTCTACAACTCACGAACCTAATCA
TTACAATCAACTCTGTGAACTCATTTCCAACAATAGTTCCAATCCGGTAA
CACCGATAGAAAAGTATCCGCGTCAGGTTTGTTTTAATAGCATCAAATAT
AAAAATTATATGCCAGGACTGGGTCAATATAAATAACACTAATTGTTATT
GTCAATATTTATTTATTTATATGATTTATTTTATGATTTGCATGTTATAA
GATTTTTATTTCAATTTATTAACTAGTCTGAGGTGCGAAGGATGAGTAGC
ATGACTGAAAGGGTAATGATTTTAAATAACACTAACATTTCTTCACGGAA
TATTGTCGTTTCAATATAATATCCAGGGCCGGTTCAAACTCTTTTATCTC
ATAATTTATTATTTCTGCTTACTTTATATTTTATTGCTAAATGTAGACAA
CGGGTAAATAAAATGCAGGACAATATCGTTGCCCAGATTTAAAATTTGTA
TTCATTTTGCAAATGTCTGAGTCGGCCCTGATAACGCGCCTCTAATCTAT
TGGAAGTTTTGTGCATTTTGACAGCTATTGCTTTTTTGTCTATTTTTTTT
ATTCGCATCTTCTGTATTTGCTGTTTTTATTTTTGATTTATATCTAAGAT
ATTCAGTCCGATTAAGAAGTTAATAAATCGTGTATCTAGTGATAGAAAGG
TATGGCTGGTTTAGAGTTAATAAAGAATTCGTGTTTCAGTTATTTTTATA
TGCCAGTTAAATAATTATAATGGTGTCTTTTGGTGATATATTTTTAATAT
TTCCCGGATTATACTTATCCGGAATTTGTTTATAATGATAAAATGAATAT
TGGTCTCATTTCAATCTAATGTTTAGTAGACTGATGAGTTTAGGAAATGC
TTTTGAATCGGCTGATGAATTACTGAAAAGTTTTGTTCCTTGGTATATTT
CAAATAGAGTTTCCTGGGCTATTTCGACATCGTCTCAACCAACTTCACCG
GGAAAAGATATATTTTAATTGAAAACACTTCAACATGTCGAGTGATAACA
AATAGTATTGAATACACTAGCTTCCATAAATTATGTGCAACGAAGACAAA
TATTATCGGCAGCTAGTACATTAAAAGTTATATTTTTCGTTATATTTACA
TTTTTTAATG
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protein sequence of SMED30017824-orf-1

>SMED30017824-orf-1 ID=SMED30017824-orf-1|Name=SMED30017824-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MISIYYIYCLKPKMSMPVIDNSSNLMNNPSMVKVKSVSGNLLEMKKSAIQ
SACIVTNANPMSPSRPAVHHRHSTTHEPNHYNQLCELISNNSSNPVTPIE
KYPRQVCFNSIKYKNYMPGLGQYK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0002109X1 cell