SMED30030350

Overview
NameSMED30030350
Smed IDSMED30030350
Length (bp)647
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



SMED30030350

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30030350SMESG000053935.1 SmedASXL_009917SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30030350SMESG000053935.1 SmedASXL_009917SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30030350SMESG000053935.1 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30030350SMESG000053935.1 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30030350SMESG000053935.1 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30030350SMESG000053935.1 dd_Smed_v4_4129_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030350SMESG000053935.1 Contig45411newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30030350SMESG000053935.1 Contig45411uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neoblastSMED30030350SMESG000053935.1 SMED_37391_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030350 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001069:25076..25802 +2757
Homology
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BLAST of SMED30030350 vs. Planmine SMEST
Match: SMESG000053935.1 (SMESG000053935.1)

HSP 1 Score: 135.576 bits (340), Expect = 1.262e-36
Identity = 73/73 (100.00%), Postives = 73/73 (100.00%), Query Frame = 1 
Query:   97 AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK 315
            AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK
Sbjct:   21 AQNLKPNKNGQKINNNPALNKKQIINSTDKVNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQK 93
The following BLAST results are available for this feature:
BLAST of SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 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 SMED30030350 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000053935.11.262e-36100.00SMESG000053935.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030350 ID=SMED30030350|Name=SMED30030350|organism=Schmidtea mediterranea sexual|type=transcript|length=647bp
GTTTTAAATACATTTAAAAAGTAACGCATCGTGAAAATGTCTAAAAGCAA
AAATCAAAAGAAATCTAATAATAAGCCTTCAAATGTTCCGGTGAAAGCTC
AAAATTTAAAACCTAATAAAAATGGACAAAAAATTAACAATAATCCAGCA
CTCAACAAAAAACAAATTATCAACTCAACTGATAAGGTCAACCAAAAACC
AGTAACTAATTCTATTGCCAAAGTTCAGCCAATCAAAACTGAATTGTCCA
AGAATGAAAGCAATGCAATTAAAAAGTCTGTTGTTGAAAAGAAAAATGTG
AAACTTCTCCAAAAAGAAATAGATATTGCTGAATCTGGTGAAGATGAAGA
CGAAGATGATATTGAATTTGAGGATGATTCTGATATTGACGATGTCGATC
TTGGCGATTCAGATGATGATCTCGATCTTGGAGATTCAGATGATGATCTT
GGAGATTCAGATGATGATCTTGGAGATTCAGATGATGATTTATCAGTTAT
GGACTTGAATTCTGATTTAGAAAGCATCGAGTTAGATGAAGATGCTATTG
ATGAAGCCGAAGTTGAAATTAAGAAAAAACCAATAAAGAAGGAATCTTCT
AAGCCAGCTGAGAAGAAGGAAGTTCCTAAACCAGCTGAGAAGAAGGA
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protein sequence of SMED30030350-orf-1

>SMED30030350-orf-1 ID=SMED30030350-orf-1|Name=SMED30030350-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=203bp
MSKSKNQKKSNNKPSNVPVKAQNLKPNKNGQKINNNPALNKKQIINSTDK
VNQKPVTNSIAKVQPIKTELSKNESNAIKKSVVEKKNVKLLQKEIDIAES
GEDEDEDDIEFEDDSDIDDVDLGDSDDDLDLGDSDDDLGDSDDDLGDSDD
DLSVMDLNSDLESIELDEDAIDEAEVEIKKKPIKKESSKPAEKKEVPKPA
EKK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..61
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 169..196
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 96..145
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 98..145
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 7..61