SMED30027209

Overview
NameSMED30027209
Smed IDSMED30027209
Length (bp)442
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30027209

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30027209 SmedASXL_074801SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30027209SMESG000078034.1 dd_Smed_v4_12031_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30027209SMESG000078034.1 dd_Smed_v4_12031_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30027209SMESG000078034.1 dd_Smed_v4_12031_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30027209SMESG000078034.1 dd_Smed_v4_12031_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
Homology
BLAST of SMED30027209 vs. Planmine SMEST
Match: SMESG000069853.1 (SMESG000069853.1)

HSP 1 Score: 87.8113 bits (216), Expect = 2.656e-21
Identity = 42/70 (60.00%), Postives = 48/70 (68.57%), Query Frame = -3
Query:   21 NQNLTQTFYWQLVEPMVSKVNYITSNVALFFRTILSLKHSFNFAYKRVPSGNLKIFVWYCLGNNHIISKL 230
            N+N  Q FY QLVEP    VNY  SN A F RTI  L+HS N  Y+R+PSG  KIFVW CLGNNHI+S +
Sbjct:    5 NRNRAQAFYRQLVEPRDRSVNYRISNSAHFLRTIYPLEHSSNVVYQRMPSGKQKIFVWGCLGNNHIVSNI 74          
BLAST of SMED30027209 vs. Planmine SMEST
Match: SMESG000003212.1 (SMESG000003212.1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.128e-11
Identity = 33/68 (48.53%), Postives = 42/68 (61.76%), Query Frame = 3
Query:   36 MIITQTIPYKYF*ITTRHPFVSKVETVF**KDRPEKESDIASNVIDFANHWFHELPIEGLC*ILIIIS 239
            M++TQ        + TRHP +S V TVF   DRP+K S IA+ +ID   H  +ELPIEGLC I I+ S
Sbjct:    1 MVVTQVPHTNILSLATRHPLLSNVGTVFEWVDRPQKVSAIANAIIDRTIHGSNELPIEGLCSISILRS 68          
BLAST of SMED30027209 vs. Planmine SMEST
Match: SMESG000074559.1 (SMESG000074559.1)

HSP 1 Score: 56.6102 bits (135), Expect = 5.140e-10
Identity = 29/51 (56.86%), Postives = 32/51 (62.75%), Query Frame = -3
Query:   78 NQNLTQTFYWQLVEPMVSKVNYITSNVALFFRTILSLKHSFNFAYKRVPSG 230
            N+N  Q FY QLV PM   VNY  SN A F RTI  L+HS N A +RVPS 
Sbjct:    5 NRNRAQAFYRQLVGPMDRSVNYSISNRAHFLRTINPLEHSSNVAQQRVPSA 55          
BLAST of SMED30027209 vs. Planmine SMEST
Match: SMESG000003297.1 (SMESG000003297.1)

HSP 1 Score: 51.2174 bits (121), Expect = 4.625e-9
Identity = 26/46 (56.52%), Postives = 33/46 (71.74%), Query Frame = -1
Query:   80 HRPSIGSSWNQWLAKSITLLAMSLSFSGRSFH*NTVSTLLTNGCRV 217
            H+ SI SS +    +SIT LA++L+F GRS H NTV TL +NGCRV
Sbjct:   19 HKSSIDSSLDPESIRSITALAIALTFCGRSTHSNTVPTLPSNGCRV 64          

HSP 2 Score: 25.7942 bits (55), Expect = 4.625e-9
Identity = 9/16 (56.25%), Postives = 14/16 (87.50%), Query Frame = -3
Query:   24 KIFVWYCLGNNHIISK 71
            KIF+W CLGN++ ++K
Sbjct:   68 KIFIWSCLGNHNDLNK 83          
The following BLAST results are available for this feature:
BLAST of SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 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 SMED30027209 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000069853.12.656e-2160.00SMESG000069853.1[more]
SMESG000003212.11.128e-1148.53SMESG000003212.1[more]
SMESG000074559.15.140e-1056.86SMESG000074559.1[more]
SMESG000003297.14.625e-956.52SMESG000003297.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027209 ID=SMED30027209|Name=SMED30027209|organism=Schmidtea mediterranea sexual|type=transcript|length=442bp
GGTGGGTTCCTGGATGGTGATAATTTTGAAATTATATGATTATTACCCAG
ACAATACCATACAAATATTTTTAGATTACCACTCGGCACCCGTTTGTAAG
CAAAGTTGAAACTGTGTTTTAGTGAAAGGATCGTCCGGAAAAAGAGAGCG
ACATTGCTAGTAATGTAATTGACTTTGCTAACCATTGGTTCCACGAGCTG
CCAATAGAAGGTCTGTGTTAGATTTTGATTATAATTTCACCATTCCTCTC
CTATCTTATTGAGGAGTTAATATATCCTTCCAACAAAAGCTAAACTTCTA
TGACACATTTGTCTCGCTGACTCATTTTAAAACCGAATAATTACAAACAG
AATACAGTCCCATCATTTTTCAAAATCTTAAAACATAATTTCTCCACCAT
TATACATTACATCATTTAGTGGTTTCATGTGGGGATTTATTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0002109X1 cell