SMED30012075

Overview
NameSMED30012075
Smed IDSMED30012075
Length (bp)1296
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 SMED30012075 (SMED30012075) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012075 (SMED30012075) 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 SMED30012075 (SMED30012075) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012075 (SMED30012075) 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




SMED30012075

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



PAGE Curations: 16

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X2 cellSMED30012075SMESG000059352.1 SMESG000059351.1 SmedASXL_007925SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v4_420_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neural progenitor cellSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v6_420_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle progenitor cellSMED30012075SMESG000059352.1 SMESG000059351.1 dd_Smed_v6_420_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
SMED30012075 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004443:20079..21618 -6375
Homology
BLAST of SMED30012075 vs. Planmine SMEST
Match: SMESG000059352.1 (SMESG000059352.1)

HSP 1 Score: 219.935 bits (559), Expect = 2.367e-70
Identity = 160/163 (98.16%), Postives = 160/163 (98.16%), Query Frame = 3
Query:  285 MGNKTGKFNVPATEKINKDEQVINEDGTVETQVVVEANGDQPKPESNGVDKTEHAPEXXXXXXXXXXXXXXXXXXXXXXASKENGVKEETPKENGVVEEPIELVKENGNXXXXXXXXXXXXTPEIHNDEVNEVSPEVTEKNDETPIANGHDTGAESSEPTEEH 773
            MGNKTGKFNVPATEKINKDEQVINEDGTVET VVVEANGDQPKPESNGVDKTEHAPEVKKKSVVSWFKKVSMRKEKKSKASKENGVKEETPKENGVVEEPIELVKENGNVEASSEKVESVET EIHNDEV EVSPEVTEKNDETPIANGHDTGAESSEPTEEH
Sbjct:    1 MGNKTGKFNVPATEKINKDEQVINEDGTVETPVVVEANGDQPKPESNGVDKTEHAPEVKKKSVVSWFKKVSMRKEKKSKASKENGVKEETPKENGVVEEPIELVKENGNVEASSEKVESVETTEIHNDEVKEVSPEVTEKNDETPIANGHDTGAESSEPTEEH 163          
BLAST of SMED30012075 vs. Planmine SMEST
Match: SMESG000051408.1 (SMESG000051408.1)

HSP 1 Score: 48.1358 bits (113), Expect = 5.247e-6
Identity = 23/28 (82.14%), Postives = 24/28 (85.71%), Query Frame = 3
Query:  261 FLKLYYIQMGNKTGKFNVPATEKINKDE 344
            FLKL YIQ  NK+GKFNVPATEK NKDE
Sbjct:  151 FLKLNYIQKENKSGKFNVPATEKTNKDE 178          
The following BLAST results are available for this feature:
BLAST of SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 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 SMED30012075 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000059352.12.367e-7098.16SMESG000059352.1[more]
SMESG000051408.15.247e-682.14SMESG000051408.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012075 ID=SMED30012075|Name=SMED30012075|organism=Schmidtea mediterranea sexual|type=transcript|length=1296bp
GTTACATTGTAAAAATCATCAATTGAAATGATTAAGCAACCTGTTAGTCA
GAAACACACGTAATACATACCTCTGTAAATTGTGACAAAACCGACGTTGC
CTGTAGTTTTCCTTTTGCTTGTCTTAGTCAATCATACAAAGAATAATTGG
TCTGACTCATTGCATAGAAGAGCCAATCAAAATCATTTATTTAACGCAGC
CATCTTGTCAGTTTATTTTATTAAACTATATTTTGGTTAGATAGCATAAA
TTGGAATTCGTTTCTGAAATTATATTACATTCAAATGGGAAATAAAACAG
GAAAATTTAATGTTCCAGCAACTGAAAAGATTAATAAAGATGAACAAGTG
ATAAATGAAGATGGAACAGTTGAAACTCAAGTTGTTGTGGAAGCTAATGG
TGACCAACCGAAACCAGAATCAAATGGTGTAGATAAAACAGAACATGCGC
CAGAGGTGAAAAAGAAAAGCGTTGTTTCGTGGTTCAAAAAAGTATCAATG
AGAAAAGAGAAAAAGTCTAAAGCATCTAAAGAAAATGGAGTTAAAGAAGA
AACTCCTAAAGAAAACGGAGTTGTTGAAGAGCCAATTGAACTTGTAAAAG
AAAATGGAAATGTTGAAGCCTCATCAGAAAAAGTTGAATCGGTTGAAACT
CCAGAAATTCATAATGATGAAGTAAACGAAGTTTCACCCGAAGTGACTGA
GAAAAACGATGAGACACCTATCGCTAATGGTCACGATACTGGTGCTGAAA
GCTCAGAACCAACAGAAGAACATTAAATGAACTTTTATTTGATTTAAGTC
TTTTGTTCTAGTCTACGCAAGTGGATCGATTTTATAACAATTCCACATAA
TTATCGTGATGCTTCTCAACTTTGTTTGATTGTATTATGTATGTCTGTTT
TTCTGATTGAAATCAGGATTTAAGTTTTTATTTTGTAGTTTTAATGTCAA
TGGAAAAGTAATGTACAGTTTTTATCTTAACCATACTCCAAATAATCTAT
TTTCGGTTTTGTAAACAAGTGCAATTAATTGCATATTTGAATCGTGTATG
CAATGAATTTAATGTTGTCAATTTTAGTTGAAGCAGTAAAAATACATTTT
TAAGAAAGTTTATTTTTATGACTAACAAATTACACATTAATAAGCAATGT
AAATGCTTGATTGTTATTGATAACTACGATTAGAAATATGGTATTCGATG
TGGCTGTTATTTTAATTTTCCAAATGACATCATCGCACGCGCTGATGATT
CAATTTGTATTAATCACGTTTGTTTTGTCAAAACTGACAAGCACTG
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protein sequence of SMED30012075-orf-1

>SMED30012075-orf-1 ID=SMED30012075-orf-1|Name=SMED30012075-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=164bp
MGNKTGKFNVPATEKINKDEQVINEDGTVETQVVVEANGDQPKPESNGVD
KTEHAPEVKKKSVVSWFKKVSMRKEKKSKASKENGVKEETPKENGVVEEP
IELVKENGNVEASSEKVESVETPEIHNDEVNEVSPEVTEKNDETPIANGH
DTGAESSEPTEEH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000012neural progenitor cell
PLANA:0000019muscle progenitor cell
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000101muscle 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: 46..100
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 109..146
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..163