SMED30025746

Overview
NameSMED30025746
Smed IDSMED30025746
Length (bp)971
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 SMED30025746 (SMED30025746) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025746 (SMED30025746) 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 SMED30025746 (SMED30025746) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30025746 (SMED30025746) 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




SMED30025746

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
intestinal phagocyteSMED30025746h1SMcG0008627 Contig4008newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025746h1SMcG0008627 Contig4008uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025746h1SMcG0020365 Contig4008newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025746h1SMcG0020365 Contig4008uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
pharynxSMED30025746h1SMcG0020365 dd_Smed_v4_7030_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025746h1SMcG0020365 dd_Smed_v4_5293_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30025746h1SMcG0020365 dd_Smed_v4_5293_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30025746h1SMcG0020365 dd_Smed_v6_7030_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30025746h1SMcG0020365 OX_Smed_1.0.08066ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025746 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002671:24462..41274 +4654
Homology
BLAST of SMED30025746 vs. Planmine SMEST
Match: SMESG000043367.1 (SMESG000043367.1)

HSP 1 Score: 422.55 bits (1085), Expect = 1.053e-150
Identity = 230/230 (100.00%), Postives = 230/230 (100.00%), Query Frame = 2
Query:   53 MSHSPKNENSKNTIENNPDRKFQNGKCPYDNIKPWNSISKYNQNSMQESYYNGNDWRYPHINFPQNLPANYSSATYYFNNNPYQCFPSYVYNPYSNDMNYVYYPVRQLQHYNNYWXXXXXXXXXXXXXXXXXFRKHRAGKQYVYNVKNDFYFNDEGEYIDDNIDDMQEMKEIETLDEEIPKEHYNYRDYCNSPSNDELCESTSMLLDRVTERAKGYLNLYSHNIHDNIRP 742
            MSHSPKNENSKNTIENNPDRKFQNGKCPYDNIKPWNSISKYNQNSMQESYYNGNDWRYPHINFPQNLPANYSSATYYFNNNPYQCFPSYVYNPYSNDMNYVYYPVRQLQHYNNYWRGSNSNRYNSHNNNNRNFRKHRAGKQYVYNVKNDFYFNDEGEYIDDNIDDMQEMKEIETLDEEIPKEHYNYRDYCNSPSNDELCESTSMLLDRVTERAKGYLNLYSHNIHDNIRP
Sbjct:    1 MSHSPKNENSKNTIENNPDRKFQNGKCPYDNIKPWNSISKYNQNSMQESYYNGNDWRYPHINFPQNLPANYSSATYYFNNNPYQCFPSYVYNPYSNDMNYVYYPVRQLQHYNNYWRGSNSNRYNSHNNNNRNFRKHRAGKQYVYNVKNDFYFNDEGEYIDDNIDDMQEMKEIETLDEEIPKEHYNYRDYCNSPSNDELCESTSMLLDRVTERAKGYLNLYSHNIHDNIRP 230          
The following BLAST results are available for this feature:
BLAST of SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 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 SMED30025746 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000043367.11.053e-150100.00SMESG000043367.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025746 ID=SMED30025746|Name=SMED30025746|organism=Schmidtea mediterranea sexual|type=transcript|length=971bp
TCTATATAAATCTTATATGAATAAATTCTAGTTTTCCTTGTTAAAAAATT
CAATGAGCCATTCACCGAAAAATGAAAACTCAAAGAACACAATCGAAAAT
AATCCAGATCGGAAATTTCAAAACGGTAAATGTCCCTACGACAATATAAA
GCCATGGAACTCTATTTCGAAATACAACCAGAATTCTATGCAAGAATCGT
ATTACAATGGTAATGATTGGCGTTATCCTCATATCAATTTTCCTCAAAAT
TTACCAGCAAACTATTCGTCTGCTACTTACTATTTCAATAATAACCCCTA
TCAATGTTTTCCTTCTTATGTATATAATCCCTATTCAAATGACATGAACT
ACGTTTATTATCCTGTTAGACAATTACAACATTACAATAATTATTGGCGT
GGATCTAATAGTAATCGCTACAATAGTCATAATAATAATAATAGGAACTT
TCGTAAACATCGCGCTGGCAAACAATATGTGTATAATGTGAAGAACGATT
TTTATTTCAATGATGAAGGAGAATATATTGACGACAACATTGACGATATG
CAGGAAATGAAAGAGATTGAAACTCTTGATGAAGAAATCCCAAAAGAGCA
TTACAATTATCGAGACTATTGTAATTCCCCTTCAAATGATGAATTATGCG
AATCAACTTCAATGTTATTGGATAGAGTTACTGAACGAGCGAAAGGCTAT
TTGAATTTATACAGTCACAATATTCATGACAACATTCGACCGTGATTCCA
AGCCCACTTAAAGAATTCGAAAAAATGTTTCATATCAACTTTCAGTTTTA
TTTTCGCGAATCATATTCTCTTTGGATTTATTTTTTGAATGATCTTTAAT
TTTGGAGCATGGTTTATATTTTTCTTTTGACTTAGATAATGTTGCTTACG
CGGTTGTTCCGATTTTGAAATAATTATTTTTGTTATGGCTATTTTATTAA
TATAATTATGCACTGAAAAAA
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protein sequence of SMED30025746-orf-1

>SMED30025746-orf-1 ID=SMED30025746-orf-1|Name=SMED30025746-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=231bp
MSHSPKNENSKNTIENNPDRKFQNGKCPYDNIKPWNSISKYNQNSMQESY
YNGNDWRYPHINFPQNLPANYSSATYYFNNNPYQCFPSYVYNPYSNDMNY
VYYPVRQLQHYNNYWRGSNSNRYNSHNNNNRNFRKHRAGKQYVYNVKNDF
YFNDEGEYIDDNIDDMQEMKEIETLDEEIPKEHYNYRDYCNSPSNDELCE
STSMLLDRVTERAKGYLNLYSHNIHDNIRP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000070intestinal phagocyte
PLANA:0000418head
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..25
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20