SMED30023243

Overview
NameSMED30023243
Smed IDSMED30023243
Length (bp)700
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 SMED30023243 (SMED30023243) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30023243 (SMED30023243) 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 SMED30023243 (SMED30023243) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023243 (SMED30023243) 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




SMED30023243

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



PAGE Curations: 41

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30023243h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30023243h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30023243h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023243h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
secretory cellSMED30023243h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30023243h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30023243h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30023243h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30023243h1SMcG0011363 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30023243h1SMcG0011363 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30023243h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30023243h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
central nervous systemSMED30023243h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30023243h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30023243h1SMcG0014660 Contig1862GPL15192PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30023243h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30023243h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30023243h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30023243h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
secretory cellSMED30023243h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
secretory cellSMED30023243h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30023243h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
head regionSMED30023243h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30023243h1SMcG0014660 Contig505uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30023243h1SMcG0014660 Contig505newmark_estsPMID:23079596
Forsthoefel et al., 2012
whole organism asexual adult colorimetric in situ hybridization evidence
pigment cellSMED30023243h1SMcG0014660 SmedASXL_008102SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30023243h1SMcG0014660 Contig11338uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023243h1SMcG0014660 Contig11338newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30023243h1SMcG0014660 dd_Smed_v4_1555_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023243h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023243h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023243h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023243h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30023243h1SMcG0014660 dd_Smed_v4_587_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023243h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30023243h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
GABAergic neuronSMED30023243h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx musculatureSMED30023243h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023243h1SMcG0014660 dd_Smed_v6_587_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023243h1SMcG0014660 dd_Smed_v4_1555_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023243h1SMcG0014660 dd_Smed_v4_587_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
SMED30023243 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001151:48426..51587 +3341
Homology
BLAST of SMED30023243 vs. Planmine SMEST
Match: SMESG000009320.1 (SMESG000009320.1)

HSP 1 Score: 374.4 bits (960), Expect = 4.627e-125
Identity = 206/213 (96.71%), Postives = 206/213 (96.71%), Query Frame = -1
Query:   62 TALHIXVSHECDXQIIEMLLKRXDLNINKPLFNQTTALHVANKMKLFHISNLLKKFNAIDLASNDFXXXXXXXXXXXXXXDINSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRNXXVKKIELNWING 700
            TALHI VSHECD QIIEMLLKR DLNINKPL NQTTALHVANKMKLFHISNLLKKFNAIDLAS DFEMQESDEDCEEEIEDINSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRN  VKKIELNWING
Sbjct:  624 TALHIAVSHECDIQIIEMLLKRTDLNINKPLSNQTTALHVANKMKLFHISNLLKKFNAIDLASTDFEMQESDEDCEEEIEDINSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRNDLVKKIELNWING 836          
BLAST of SMED30023243 vs. Planmine SMEST
Match: SMESG000009320.1 (SMESG000009320.1)

HSP 1 Score: 371.703 bits (953), Expect = 4.428e-124
Identity = 195/213 (91.55%), Postives = 199/213 (93.43%), Query Frame = -1
Query:   62 TALHIXVSHECDXQIIEMLLKRXDLNINKPLFNQTTALHVANKMKLFHISNLLKKFNAIDLASNDFXXXXXXXXXXXXXXDINSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRNXXVKKIELNWING 700
            TALHI VSHECD QIIEMLLKR DLNINKPL NQTTALHVANKMKLFHISNLLKKFNAIDLAS DFEM+  ++  EE  + INSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRN  VKKIELNWING
Sbjct:  624 TALHIAVSHECDIQIIEMLLKRTDLNINKPLSNQTTALHVANKMKLFHISNLLKKFNAIDLASTDFEMESDEDCEEEIED-INSLHCDSIQSESSNNPITEIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQLVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRNDLVKKIELNWING 835          
The following BLAST results are available for this feature:
BLAST of SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 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 SMED30023243 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000009320.14.627e-12596.71SMESG000009320.1[more]
SMESG000009320.14.428e-12491.55SMESG000009320.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023243 ID=SMED30023243|Name=SMED30023243|organism=Schmidtea mediterranea sexual|type=transcript|length=700bp
TTTTTTTTTTTTTTTTTTAATCTTATTTTTACGTTTGTAAATAAATGTCA
AATTTAAATCACCCATTTATCCAATTCAGTTCAATCTTCTTTACCNANNC
ATTTCTGCCAATTTCACGCAATTTATCGATTAGCTGACCACCGGAATTTG
GGAGGCAATTAAACCGATCCAACAACTCACAGATATCTTTCTTGTTATCA
TTCCCGTTGCTATATTTATTGAAAAGCGATTTATAAGTTGGTCTCACCAG
CTGCTGAAGTTCTTTCACTGTTAAAGTGGGCCCGCTGGACAACATTAAAA
TGTCAATAACTTTCATTTTTATTTCTCCTTTCAAGCTTAACTCCTTCAAT
GAATTGGTAATCATATTGATGGTTCGATTAGAACTCTCATCTTTTATTTC
GGTTATTGGATTATTACTTGATTCCGATTGAATGCTGTCGCAATGAAGGG
AATTGATATCTTCAATTTCTTCTTCACAGTCTTCGTCAGATTCCTGCATT
TCAAAGTCATTGCTTGCTAAGTCAATTGCATTAAATTTCTTCAATAAATT
GGAAATATGAAAAAGCTTCATTTTGTTAGCAACATGCAAAGCTGTTGTCT
GGTTAAACAGTGGTTTATTGATATTAAGATCTGNTCTTTTCAAAAGCATT
TCGATAATTTGNATGTCACATTCGTGGCTCACGGNAATATGAAGTGCAGT
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protein sequence of SMED30023243-orf-1

>SMED30023243-orf-1 ID=SMED30023243-orf-1|Name=SMED30023243-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=214bp
TALHIXVSHECDXQIIEMLLKRXDLNINKPLFNQTTALHVANKMKLFHIS
NLLKKFNAIDLASNDFEMQESDEDCEEEIEDINSLHCDSIQSESSNNPIT
EIKDESSNRTINMITNSLKELSLKGEIKMKVIDILMLSSGPTLTVKELQQ
LVRPTYKSLFNKYSNGNDNKKDICELLDRFNCLPNSGGQLIDKLREIGRN
XXVKKIELNWING*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000103central nervous system
PLANA:0000105secretory cell
PLANA:0000420parapharyngeal region
PLANA:0000463cholinergic neuron
PLANA:0000464GABAergic neuron
PLANA:0000478pharynx musculature
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR036770Ankyrin_rpt-contain_sf
IPR020683Ankyrin_rpt-contain_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036770Ankyrin repeat-containing domain superfamilyGENE3DG3DSA:1.25.40.20coord: 1..82
e-value: 3.6E-6
score: 28.2
IPR036770Ankyrin repeat-containing domain superfamilySUPERFAMILYSSF48403Ankyrin repeatcoord: 1..58