SMED30024623

Overview
NameSMED30024623
Smed IDSMED30024623
Length (bp)1846
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 SMED30024623 (SMED30024623) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024623 (SMED30024623) 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 SMED30024623 (SMED30024623) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024623 (SMED30024623) 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



SMED30024623

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30024623SMESG000004071.1 Contig1198newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024623SMESG000004071.1 Contig1198uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024623SMESG000054962.1 Contig1198newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30024623SMESG000054962.1 Contig1198uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
nervous systemSMED30024623SMESG000004071.1 dd_Smed_v4_8958_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30024623SMESG000004071.1 dd_Smed_v4_8958_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30024623SMESG000004071.1 dd_Smed_v4_8958_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30024623 dd_Smed_v4_11607_0_1dd_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 SMED30024623 vs. Planmine SMEST
Match: SMESG000004071.1 (SMESG000004071.1)

HSP 1 Score: 259.225 bits (661), Expect = 9.215e-82
Identity = 139/163 (85.28%), Postives = 142/163 (87.12%), Query Frame = 2 
Query:    2 NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDEG*K*FYCFLLMFFELRIQILSFNGAYRKDDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNEIVKLQEELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI 490
            NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDE  K        F+ L     + N    +DDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNEIVKLQEELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI
Sbjct:    2 NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDEESK--------FYPLTAH--TENLCSLEDDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNEIVKLQEELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI 154

HSP 2 Score: 250.366 bits (638), Expect = 1.807e-78
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 1 
Query: 1429 QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH 1788
            QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH
Sbjct:  161 QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH 280
[Close]
BLAST of SMED30024623 vs. Planmine SMEST
Match: SMESG000004071.1 (SMESG000004071.1)

HSP 1 Score: 250.366 bits (638), Expect = 1.694e-78
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 1 
Query: 1429 QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH 1788
            QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH
Sbjct:  155 QRLICLLSKYEHFEMKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNSQLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECPKLKNIH 274

HSP 2 Score: 241.891 bits (616), Expect = 3.100e-75
Identity = 133/163 (81.60%), Postives = 136/163 (83.44%), Query Frame = 2 
Query:    2 NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDEG*K*FYCFLLMFFELRIQILSFNGAYRKDDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNEIVKLQEELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI 490
            NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDE  K        F+ L     + N    +DDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNE      ELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI
Sbjct:    2 NETDLSEGFGFKPGSLSKVKSVEKNFNLLSDEESK--------FYPLTAH--TENLCSLEDDFQTLKQVLKSKYDAINIFKKISHSMNMERISLEKHLLEITLLFKNE------ELEHSQSAFYENLKIWTARFKDLDTECIMLKEELMNKSNSIQKLTSDNI 148
The following BLAST results are available for this feature:
BLAST of SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 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 SMED30024623 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000004071.19.215e-8285.28SMESG000004071.1[more]
SMESG000004071.11.694e-78100.00SMESG000004071.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024623 ID=SMED30024623|Name=SMED30024623|organism=Schmidtea mediterranea sexual|type=transcript|length=1846bp
GAACGAAACAGATTTGTCCGAAGGATTTGGTTTTAAGCCAGGAAGTTTGT
CTAAAGTTAAGAGCGTAGAAAAAAACTTCAATTTGCTAAGTGATGAAGGT
TAAAAATGATTTTATTGTTTTTTATTAATGTTTTTTGAATTGAGAATCCA
AATTTTATCCTTTAACGGCGCATACAGAAAAGATGATTTTCAAACTTTAA
AGCAAGTGCTCAAGTCCAAATATGATGCCATAAATATTTTCAAAAAAATT
AGCCACTCAATGAATATGGAGCGAATAAGTTTAGAAAAACATTTATTGGA
AATAACTCTCCTCTTTAAAAATGAAATCGTTAAATTACAGGAAGAACTCG
AACATTCTCAATCTGCTTTTTATGAAAATTTAAAAATATGGACTGCTAGA
TTTAAAGATTTGGATACAGAATGCATCATGCTTAAAGAAGAATTAATGAA
CAAGTCCAACTCCATCCAAAAACTTACCTCCGACAATATTGGTAATTACA
TTTTTATTTAATTATTATTTTTTCATTTAGATTGAGTTCGAGCTTTGAAA
AGTAGGATAATTTTTTTTTTAATTTACTAGTTATCAGTACAAGACAAATG
TTTATATAATTTATTTTCTCACGAAAGATATTTTTTACATCTTTATATAT
GGACTTATACTGCGTATCATCTTGGATAGATTCAAACTCATTCTTTATTC
ATGCTAATTAATCTTATTCATCTGGTTATTACAAATTTTTTTTCAATAAA
ATATTTTAGTCCCTTTTTGATCATCATGATCATTTACCTTTGACATTCCC
ATTTACAGCGGTTTATACGAGAACCATTAGTCTGTTTAAGCGGTATTCAC
AATAACAAAGAACTCCAAATACAGGCTTCAAAAATATTATATAAATTTTC
ATGAGTCACTTTATTTTAACAAAAACAGGCAGAATATTGAAAAAAGAAAA
AACAACTTTGTGCCACTTGTAGTTGATTTTAATATAAAAAACGTATTTGA
CTTCATGATATTCAACCTAGTGACGAGTGTCAGTGCTGGTACGCAGATAG
CAGTAAAATTTCATGTTGAAATTGAAAAACCGATTGTCGGGATGAAATAT
TGTCAAACATACAAAGATCTAGTAACACCTTTATTAGACAGGAAAGCATC
TTGTGACTTAAACCGGAAGTCTGGGTCATAATGAGTTTGTCTAGAACAAA
TTACACTACTCATTGAATAATACGCAAAACTCAACCAGCGCGGTATTCCA
CCTGAACGAATTTGCTACTCTGTTTCTTGGGCAAGGCATACCTATATTTG
TTGCGTAAGCGGGACAGCCATAATATGTCAATTCCTATACAAATGCAAAT
TCAATGATATGAAATATGCAATGATACAAGAGATATGTTTTCATCGAATT
GTTAACTTTAGAACTATTGAAAGAAAAGCAAAGACTCATATGTTTGTTGT
CGAAATATGAACATTTCGAGATGAAGACAAATTACAATTACGGAAATGAA
GCAAAACAAGATCTCATACAAACTGGAAAACGCCAACGTGAGAAGTTATA
TAAAAATGAAAAGTTCTTAAGATATCATTCTTTTGACTCATATCCATGCT
CCACAAAGCCTTCAAATTCTCAGTTAAAATGCAGATGTGAAAAATATCAG
ACTGAAGATACATTAGATGAAACCTATATAATGGTAGAAGCATACAAAAT
TGCTTTCGAGGAATTATTAGCAAAAAATAGAGAATTGACATTGAAATTTA
CAAAATCTGATGAATGTCCGAAATTAAAAAATATTCATTGATGCTATACC
CAAGAAATACTGGTGTATGAAATATAAAATTATTATTTAAAAAAAA
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protein sequence of SMED30024623-orf-1

>SMED30024623-orf-1 ID=SMED30024623-orf-1|Name=SMED30024623-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=128bp
MFFELRIQILSFNGAYRKDDFQTLKQVLKSKYDAINIFKKISHSMNMERI
SLEKHLLEITLLFKNEIVKLQEELEHSQSAFYENLKIWTARFKDLDTECI
MLKEELMNKSNSIQKLTSDNIGNYIFI*
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protein sequence of SMED30024623-orf-2

>SMED30024623-orf-2 ID=SMED30024623-orf-2|Name=SMED30024623-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MKTNYNYGNEAKQDLIQTGKRQREKLYKNEKFLRYHSFDSYPCSTKPSNS
QLKCRCEKYQTEDTLDETYIMVEAYKIAFEELLAKNRELTLKFTKSDECP
KLKNIH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0003117parapharyngeal cell