SMED30023587

Overview
NameSMED30023587
Smed IDSMED30023587
Length (bp)1329
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 SMED30023587 (SMED30023587) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023587 (SMED30023587) 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 SMED30023587 (SMED30023587) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023587 (SMED30023587) 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



SMED30023587

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 phagocyteSMED30023587h1SMcG0000031 Contig3155newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0000031 Contig3155uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015179 Contig3155newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015179 Contig3155uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015181 Contig3155newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015181 Contig3155uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015180 Contig3155newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023587h1SMcG0015180 Contig3155uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
epidermisSMED30023587h1SMcG0000031 dd_Smed_v4_10428_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023587 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002169:16962..21086 -6604
Homology
[Close]
BLAST of SMED30023587 vs. Planmine SMEST
Match: SMESG000029730.1 (SMESG000029730.1)

HSP 1 Score: 438.343 bits (1126), Expect = 7.216e-155
Identity = 230/230 (100.00%), Postives = 230/230 (100.00%), Query Frame = 1 
Query:  103 MSNVIVTNPFDQAFRKEILSSSNFTISELKSENYSLNLNNIASEPNSAESVKVTVTNFVSDQEELLEDSDFNYLTKLNNKVDDSGNSFSHSLKSDIQNALIKKMKCQTKKVGSKFGGCRHQSHTNIKLPFPLDSERYHXXXXXXXXXXXXYSPSDSDSKRKNRDAAKKSRQRKKLYIAQLEKQIHQFKKNEKGFQSKLRDAEKTIQYLNNVIVQLRKNESDSLPNADFDK 792
            MSNVIVTNPFDQAFRKEILSSSNFTISELKSENYSLNLNNIASEPNSAESVKVTVTNFVSDQEELLEDSDFNYLTKLNNKVDDSGNSFSHSLKSDIQNALIKKMKCQTKKVGSKFGGCRHQSHTNIKLPFPLDSERYHNCNNNNNNNNNNYSPSDSDSKRKNRDAAKKSRQRKKLYIAQLEKQIHQFKKNEKGFQSKLRDAEKTIQYLNNVIVQLRKNESDSLPNADFDK
Sbjct:    1 MSNVIVTNPFDQAFRKEILSSSNFTISELKSENYSLNLNNIASEPNSAESVKVTVTNFVSDQEELLEDSDFNYLTKLNNKVDDSGNSFSHSLKSDIQNALIKKMKCQTKKVGSKFGGCRHQSHTNIKLPFPLDSERYHNCNNNNNNNNNNYSPSDSDSKRKNRDAAKKSRQRKKLYIAQLEKQIHQFKKNEKGFQSKLRDAEKTIQYLNNVIVQLRKNESDSLPNADFDK 230
The following BLAST results are available for this feature:
BLAST of SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 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 SMED30023587 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029730.17.216e-155100.00SMESG000029730.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023587 ID=SMED30023587|Name=SMED30023587|organism=Schmidtea mediterranea sexual|type=transcript|length=1329bp
TAATGATGGATAATATTACCAATATGAATTATTATTAAAATATTAATTTA
TTTAATTTAATTTTAATATTTGATTTGGTAATCAAAATATTATAGAAATT
TTATGAGTAACGTTATTGTAACAAATCCATTCGATCAGGCATTTAGAAAA
GAAATACTGAGTTCTTCAAATTTTACAATTTCAGAGTTAAAATCCGAAAA
CTATTCCTTAAACCTTAACAATATCGCATCAGAACCAAATTCAGCCGAAT
CAGTCAAAGTAACAGTTACAAATTTTGTATCTGATCAAGAAGAACTGTTG
GAAGATTCAGATTTTAATTATCTCACCAAACTTAATAATAAAGTCGACGA
CTCAGGAAATTCCTTCTCACATTCTCTCAAATCTGATATCCAGAATGCTT
TAATCAAGAAAATGAAATGTCAAACGAAAAAAGTCGGATCGAAATTCGGC
GGATGCCGACATCAATCCCACACAAATATCAAATTGCCATTTCCGTTAGA
TTCCGAACGATATCATAACTGCAACAATAACAATAACAATAATAATAATA
ATTATTCACCCAGTGACTCAGATTCAAAACGGAAAAACCGAGACGCAGCT
AAAAAGTCTCGACAACGAAAAAAATTATATATAGCTCAGTTAGAGAAACA
AATTCATCAATTTAAAAAAAATGAGAAAGGTTTTCAGAGCAAATTAAGGG
ATGCTGAGAAAACTATCCAATATTTGAATAATGTCATTGTACAGTTGCGG
AAAAACGAGTCCGATTCCCTTCCAAATGCAGATTTCGACAAATAAATTGC
TTTCTATCCGACATTTAGAGTGAATTTATACATAAAATGTGGTCTAATAA
ACTTTTGAACTATTTTGGTCATTTGTGCTACATTCTTTGTTCAACAGCTT
TATTATTAATATTAATAATTGAATTTTATTTTCCCAATGGTTTTGATTAG
TTCTATTATTTGATGTTTATTGGCGCATTTACGGTGCCGAATCAATTTGC
TATTTGATCTCTGTGATCAGATCGGGTAACATATATGACAATCTATAATA
TAATGCCCATTAATAACATAATGATTTCATTTATTTTTATTAATTATATA
TTACTGAATATTTGTAATTGAAATTTGCTTTTGATGAACTCTTTCAAAGG
TTCTCGATGGAGTCAAGATTGATCAGCAAGGAGGATTCTGGGAAACGGTC
CTGTAACCAAAATGTAGTGCCAAATTTGATAGCAGTATTTTATATTAAAT
GAAGGATGGAAAATTGAAAATGAACACAAAACGTCAAAAATAGTTAAAGT
ACAAAAATTTTAAAATTAATTTTGATCGG
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protein sequence of SMED30023587-orf-1

>SMED30023587-orf-1 ID=SMED30023587-orf-1|Name=SMED30023587-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=231bp
MSNVIVTNPFDQAFRKEILSSSNFTISELKSENYSLNLNNIASEPNSAES
VKVTVTNFVSDQEELLEDSDFNYLTKLNNKVDDSGNSFSHSLKSDIQNAL
IKKMKCQTKKVGSKFGGCRHQSHTNIKLPFPLDSERYHNCNNNNNNNNNN
YSPSDSDSKRKNRDAAKKSRQRKKLYIAQLEKQIHQFKKNEKGFQSKLRD
AEKTIQYLNNVIVQLRKNESDSLPNADFDK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR004827bZIP
Vocabulary: molecular function
TermDefinition
GO:0003700transcription factor activity, sequence-specific DNA binding
GO:0043565sequence-specific DNA binding
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 177..218
NoneNo IPR availableGENE3DG3DSA:1.20.5.170coord: 157..213
e-value: 1.5E-9
score: 40.0
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 142..172
NoneNo IPR availableSUPERFAMILYSSF57959Leucine zipper domaincoord: 159..212
IPR004827Basic-leucine zipper domainSMARTSM00338brlzneucoord: 154..214
e-value: 2.5E-5
score: 33.7
IPR004827Basic-leucine zipper domainPFAMPF00170bZIP_1coord: 159..209
e-value: 2.9E-9
score: 36.9
IPR004827Basic-leucine zipper domainPROSITEPS00036BZIP_BASICcoord: 159..172
IPR004827Basic-leucine zipper domainPROSITEPS50217BZIPcoord: 159..215
score: 8.944