SMED30024160

Overview
NameSMED30024160
Smed IDSMED30024160
Length (bp)778
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 SMED30024160 (SMED30024160) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024160 (SMED30024160) 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 SMED30024160 (SMED30024160) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024160 (SMED30024160) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30024160

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pigment cellSMED30024160h1SMcG0003696 SmedASXL_009503SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017		whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30024160h1SMcG0003696 Contig55100uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30024160h1SMcG0003696 Contig55100newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
pharynxSMED30024160h1SMcG0003696 dd_Smed_v4_142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30024160h1SMcG0003696 dd_Smed_v4_142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024160h1SMcG0003696 dd_Smed_v4_142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024160h1SMcG0003696 dd_Smed_v4_142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024160h1SMcG0003696 dd_Smed_v4_142_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30024160h1SMcG0003696 dd_Smed_v4_1394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024160h1SMcG0003696 dd_Smed_v4_1394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30024160h1SMcG0003696 dd_Smed_v4_1394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024160h1SMcG0003696 dd_Smed_v4_1394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
intestinal phagocyteSMED30024160h1SMcG0003696 dd_Smed_v6_1394_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30024160h1SMcG0003696 dd_Smed_v6_1394_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gamma neoblastSMED30024160h1SMcG0003696 dd_Smed_v6_142_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
intestinal phagocyteSMED30024160h1SMcG0003696 dd_Smed_v6_142_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pigment cellSMED30024160h1SMcG0003696 dd_Smed_v6_142_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30024160h1SMcG0003696 dd_Smed_v6_142_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30024160h1SMcG0003696 dd_Smed_v6_142_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30024160 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.016857:466..1244 -3833
Homology
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BLAST of SMED30024160 vs. Planmine SMEST
Match: SMESG000046560.1 (SMESG000046560.1)

HSP 1 Score: 298.516 bits (763), Expect = 1.165e-103
Identity = 143/145 (98.62%), Postives = 144/145 (99.31%), Query Frame = 1 
Query:  220 RNRVPDEIEIFPCRNGTAHCMYGHCVYLKLRWEDDIRESFDCECHKNYFGKACNKKKSLNYFFNRLKKQSVPPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYDGDGHEHKHSDNDGHDHKHEEQDEDLTQE 654
            RNRVPDEIEIFPCRNGTAHCMYGHCVYLKLRWEDDIRESFDCECHKNYFGKACNKKKSLNYFFNRLKKQSV PAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHY+GDGHEHKHSDNDGHDHKHEEQDEDLTQE
Sbjct:   21 RNRVPDEIEIFPCRNGTAHCMYGHCVYLKLRWEDDIRESFDCECHKNYFGKACNKKKSLNYFFNRLKKQSVSPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYNGDGHEHKHSDNDGHDHKHEEQDEDLTQE 165
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BLAST of SMED30024160 vs. Planmine SMEST
Match: SMESG000046560.1 (SMESG000046560.1)

HSP 1 Score: 162.925 bits (411), Expect = 3.990e-51
Identity = 80/82 (97.56%), Postives = 81/82 (98.78%), Query Frame = 1 
Query:  409 NRLKKQSVPPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYDGDGHEHKHSDNDGHDHKHEEQDEDLTQE 654
            NRLKKQSV PAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHY+GDGHEHKHSDNDGHDHKHEEQDEDLTQE
Sbjct:   20 NRLKKQSVSPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYNGDGHEHKHSDNDGHDHKHEEQDEDLTQE 101
[Close]
BLAST of SMED30024160 vs. Planmine SMEST
Match: SMESG000010944.1 (SMESG000010944.1)

HSP 1 Score: 162.925 bits (411), Expect = 3.990e-51
Identity = 80/82 (97.56%), Postives = 81/82 (98.78%), Query Frame = 1 
Query:  409 NRLKKQSVPPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYDGDGHEHKHSDNDGHDHKHEEQDEDLTQE 654
            NRLKKQSV PAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHY+GDGHEHKHSDNDGHDHKHEEQDEDLTQE
Sbjct:   20 NRLKKQSVSPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYNGDGHEHKHSDNDGHDHKHEEQDEDLTQE 101
The following BLAST results are available for this feature:
BLAST of SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 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 SMED30024160 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000046560.11.165e-10398.62SMESG000046560.1[more]
SMESG000046560.13.990e-5197.56SMESG000046560.1[more]
SMESG000010944.13.990e-5197.56SMESG000010944.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024160 ID=SMED30024160|Name=SMED30024160|organism=Schmidtea mediterranea sexual|type=transcript|length=778bp
GAATAATTATGAGATTTTTATTATTAACTTTTTTGTTAATATTTTTATTA
ACAGTCATTCACGCAAATAGGTAAGGTCTTTTGAATCTGGAACTGATTTA
TGATTTGCAATTAAATTTTTTCTTATCTAAATTCTAATTAATTTAGTTAA
TTTAGCGTTGATTAAAATATGATTGCAATGCATGTTTATAATGAATAATA
TATATCAAGTAAATCATTAAGGAATAGAGTTCCAGATGAAATAGAAATAT
TCCCATGTAGAAATGGCACAGCTCATTGCATGTATGGCCACTGTGTTTAT
CTTAAATTGAGATGGGAAGACGATATTCGAGAATCTTTTGATTGTGAATG
CCATAAAAATTATTTTGGAAAAGCATGCAATAAAAAAAAATCGCTTAATT
ATTTTTTCAATAGATTAAAAAAGCAATCGGTGCCACCAGCAGAAGAAGAT
GAATTTGAACAGATTTCTGAAGAGTTAGACGAATTTGAAAATCCAAGAAT
TAAGCGGTCGGTTGCACACCCTACAGATCAAGACCATTGGCATGATGATG
ATGGCAAAGTTCATTATGATGGCGATGGCCATGAACATAAGCATTCGGAT
AATGATGGGCATGACCATAAACATGAAGAACAGGATGAGGATTTGACCCA
AGAGTAGTTTGTCACAATTTTTTTTTAGTGTCAACTACATTGAAAATATT
TATCAAACGATTAATTAAAATAAATAAGTCTACATTTGAGACCTTGTTGA
TATTTGATTTTATACCATGATTTCTTCC
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protein sequence of SMED30024160-orf-1

>SMED30024160-orf-1 ID=SMED30024160-orf-1|Name=SMED30024160-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=126bp
MYGHCVYLKLRWEDDIRESFDCECHKNYFGKACNKKKSLNYFFNRLKKQS
VPPAEEDEFEQISEELDEFENPRIKRSVAHPTDQDHWHDDDGKVHYDGDG
HEHKHSDNDGHDHKHEEQDEDLTQE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000039gamma neoblast
PLANA:0000070intestinal phagocyte
PLANA:0000429neoblast
PLANA:0002075pigment cell
PLANA:0003116parenchymal cell
PLANA:0007528glial 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: 70..125