SMED30022793

Overview
NameSMED30022793
Smed IDSMED30022793
Length (bp)1063
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



SMED30022793

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
epidermisSMED30022793 dd_Smed_v4_9748_0_3dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30022793 dd_Smed_v4_9748_0_3dd_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
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BLAST of SMED30022793 vs. Planmine SMEST
Match: SMESG000058739.1 (SMESG000058739.1)

HSP 1 Score: 48.521 bits (114), Expect = 2.606e-7
Identity = 22/29 (75.86%), Postives = 23/29 (79.31%), Query Frame = -2 
Query:  913 MIPAKWPARSRWSLCQRNDLF*ETEGLSE 999
            MIPAKWPARSRWSLC+RNDL    EGL  
Sbjct:    1 MIPAKWPARSRWSLCRRNDLSYTIEGLDN 29
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BLAST of SMED30022793 vs. Planmine SMEST
Match: SMESG000057321.1 (SMESG000057321.1)

HSP 1 Score: 47.3654 bits (111), Expect = 1.121e-6
Identity = 32/70 (45.71%), Postives = 40/70 (57.14%), Query Frame = 2 
Query:    2 EMFNFKITNLQLIVRIMSKV-DKEYTNT*I*QQLKHYQNHVIHGIS*MTARNFLL--ILGSLAYLSCV*G 202
            EM  F+I+N QLIVRIMS+   + Y  T          NHVIH IS  TARNF+L  I+G+L     + G
Sbjct:    6 EMLYFRISNPQLIVRIMSEARQRTYWYTKGNDNWTLLANHVIHEISQTTARNFILSGIIGTLVAFEEIGG 75
The following BLAST results are available for this feature:
BLAST of SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 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 SMED30022793 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000058739.12.606e-775.86SMESG000058739.1[more]
SMESG000057321.11.121e-645.71SMESG000057321.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022793 ID=SMED30022793|Name=SMED30022793|organism=Schmidtea mediterranea sexual|type=transcript|length=1063bp
TGAAATGTTTAACTTTAAGATTACCAATTTACAACTTATTGTAAGAATAA
TGTCGAAAGTTGACAAAGAATACACCAATACATAAATTTAACAACAACTT
AAACACTATCAGAATCACGTAATTCACGGAATATCATAGATGACTGCAAG
GAATTTTCTTCTGATATTGGGATCATTGGCGTACCTTAGTTGCGTTTGAG
GAAATCCGAGGAGAGCCGGTCGACTATCCATTTAAATCCAATCGACTACA
TAGAAAACCATTGATAGACTCCCAATCATCATAAAGCTAAGCAAAACTCC
CTCGAACCGCTCATGGAACGACTGATAAGGAATCCGATCGAAATCCACAT
GTATAATAGTAATGAGCCAACTAAATAGTATTTTTGGGGAAGATCGACAG
ACACTAAATTAATGCCGAATCCCGGAGATAAATACCAATCAATACAACCC
AACTGATAATAAATTCATTTGACACTTCATAAATGTCAATCGATAATAGT
GGCAGAATTTCCCCAACATCTCTCCTCGACGACGCCGGTGTACAGACAGA
TCACAAAATTTTTCTATCGCTTCAGACACACATACCCGATGTATAGGACG
ACATGTTTGAAATATCCAGTCTGTCAATAATACGCCAAGAATAAGTTCGC
AGATCTCTAAAATATTTAACGAGCAAGGAGAAGAAGAAATTATTTCTATG
AAAACTAACAGGACGTCACACGAAGGTAGTTATTTAAATCTTGTTTCTTA
TAAGATTAATTTTATGTCCGAGTACAAGCATCCAAACGTGACCCCAGATA
ACAATTTACTATCTGTGAGGACCCGAAGACAAGGTCGACCTGGAGATTAC
AATGAAACCCTGTCATGTAATACAAATGCACTCGTTTAACTGATTTTTCT
TTTGATGAATTCCTCAGACAGTCCCTCTGTTTCTTAGAATAAGTCGTTGC
GTTGACATAGTGACCATCGACTTCTTGCGGGCCATTTGGCAGGGATCATT
GAATCCAGTTTTCTTTACAATCTTGTAATTTATATACCTTGTCTGCTTTT
CGTCTTTAGTTAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast