SMED30003533

Overview
NameSMED30003533
Smed IDSMED30003533
Length (bp)1709
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 SMED30003533 (SMED30003533) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003533 (SMED30003533) 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 SMED30003533 (SMED30003533) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003533 (SMED30003533) 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



SMED30003533

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30003533SMESG000074376.1 SmedASXL_071880SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30003533SMESG000074376.1 SmedASXL_071880SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003533 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003472:2586..4301 -7231
v31.011210:19039..20754 +7130
Homology
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BLAST of SMED30003533 vs. Planmine SMEST
Match: SMESG000074376.1 (SMESG000074376.1)

HSP 1 Score: 250.366 bits (638), Expect = 4.224e-78
Identity = 118/127 (92.91%), Postives = 124/127 (97.64%), Query Frame = 1 
Query: 1144 QARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNLENCQILSNEQSQN 1524
            + ++ADI TTVEHCGYCH+SLK+A+DAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNL NCQILSNEQSQN
Sbjct:  219 KTKNADIHTTVEHCGYCHVSLKSANDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNLANCQILSNEQSQN 345
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BLAST of SMED30003533 vs. Planmine SMEST
Match: SMESG000067725.1 (SMESG000067725.1)

HSP 1 Score: 224.557 bits (571), Expect = 3.779e-68
Identity = 104/119 (87.39%), Postives = 112/119 (94.12%), Query Frame = 1 
Query: 1144 QARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNLENCQI 1500
            +ARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRN+ELWC +CQISFTNQ+FLDLHL GFKHFVR+NRGN APEGAFGERL+KMRAKLQ+LKQSRK KKSSN E  Q+
Sbjct:  213 KARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNFELWCDVCQISFTNQSFLDLHLTGFKHFVRVNRGNSAPEGAFGERLMKMRAKLQSLKQSRKEKKSSNDEKRQL 331
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BLAST of SMED30003533 vs. Planmine SMEST
Match: SMESG000067725.1 (SMESG000067725.1)

HSP 1 Score: 224.557 bits (571), Expect = 4.300e-68
Identity = 104/119 (87.39%), Postives = 112/119 (94.12%), Query Frame = 1 
Query: 1144 QARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNLENCQI 1500
            +ARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRN+ELWC +CQISFTNQ+FLDLHL GFKHFVR+NRGN APEGAFGERL+KMRAKLQ+LKQSRK KKSSN E  Q+
Sbjct:  216 KARSADIPTTVEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNFELWCDVCQISFTNQSFLDLHLTGFKHFVRVNRGNSAPEGAFGERLMKMRAKLQSLKQSRKEKKSSNDEKRQL 334
[Close]
BLAST of SMED30003533 vs. Planmine SMEST
Match: SMESG000067728.1 (SMESG000067728.1)

HSP 1 Score: 68.9366 bits (167), Expect = 1.814e-12
Identity = 33/94 (35.11%), Postives = 55/94 (58.51%), Query Frame = 1 
Query: 1174 VEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRLNRGN-QAPEGAFGERLIKMRAKLQNLK 1452
            +E CG C  SL   SDA+ HY ++ H L +   + N   WC IC+I+  +++ L++HL GF+H+  LNR    +  G + E+++  R K + L+
Sbjct:  210 MEFCGLCDQSLSGISDAVDHYNSENH-LKLVKNNEN-SCWCNICKITLPDESLLEIHLKGFRHYRILNREECISKTGTYKEKMLYKRMKQKELR 301
[Close]
BLAST of SMED30003533 vs. Planmine SMEST
Match: SMESG000067728.1 (SMESG000067728.1)

HSP 1 Score: 52.7582 bits (125), Expect = 3.125e-7
Identity = 23/61 (37.70%), Postives = 36/61 (59.02%), Query Frame = 1 
Query: 1174 VEHCGYCHMSLKNASDAIAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGF 1356
            +E CG C  SL   SDA+ HY ++ H L +   + N   WC IC+I+  +++ L++HL  F
Sbjct:  210 MEFCGLCDQSLSGISDAVDHYNSENH-LKLVKNNEN-SCWCNICKITLPDESLLEIHLKEF 268
The following BLAST results are available for this feature:
BLAST of SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 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 SMED30003533 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074376.14.224e-7892.91SMESG000074376.1[more]
SMESG000067725.13.779e-6887.39SMESG000067725.1[more]
SMESG000067725.14.300e-6887.39SMESG000067725.1[more]
SMESG000067728.11.814e-1235.11SMESG000067728.1[more]
SMESG000067728.13.125e-737.70SMESG000067728.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003533 ID=SMED30003533|Name=SMED30003533|organism=Schmidtea mediterranea sexual|type=transcript|length=1709bp
GGTAAGCATAAACGCAAAAGTTCTGCCGAAGTCAAAGATGAGCCTGCTGA
GAAAAAGGTTAATTTTTTACTATTAACATAAATGATTTTTGAATGATTTT
CTTAAAATGCGAGGAATTTTATTTAGTGTTGAAAAAGTCATGAAATTTCG
CATTTCAAGCTTAATATGTATTTTGTTAAAGAAATATTTATCAGAACTAA
TTTATATTTTTAATTCATTTTATTACTAATTGTATTAATTACTATCAATG
AAATCCAATAAGCTATATCAAGTGATAAATTATAAATAATCATTTAATTA
ACTAAAAATATTTATAGATTTTTATTTTTCAATAAGTATAATTTTTTTCT
GCCTAAAACAGTTCGAAGACTGATTTAAACATGATCTAATAGAGTTCGAA
AGTAGATTCTTTAATAACAGATGTAATATGTTGCAAAGCATATTGTATTA
TATATCTTGATTACTTCACACAGGAGCGTTATTATTGGGGGAACGCCTGG
ATTATAAATACTATCGAACTCTCGATTTCAACTTTCAGAAACTCGTGTTG
TGAAACGCTAACCGGACTGGATAAATGCCTTCATATAGTCGACACAGCTT
CCGGTCCCCCCTCTCCTTCCGTTTGTCAGTGAACCTAGCGCATCTGTGTA
TTATAAACATTTTGCAATTCCGATTCCAACTCTTGGACAGTTTTATTGCT
TCAAATAAGTTTTTATGAGCTTTCTCTTTAATTTCAATTTTGAAACGGTG
CTGAACCAACAATCTGTAATGGCATTGTGAATTCCTTTCTCATCAGACAA
GAGTTGACAAGTCAGTTATAAATTGAGTTAGTAAAATGTCCCGGCATATT
TGTTCATCTAATGTTAGCTGGTAATGCGATTATTTCGTGGGATAGGGCAA
ATTGTGCACTATTCGATAGGGGAGATCCGTTTCTAGGCAACATTATGAAA
TGACAAAGTTATTCACACGATATGAATGATTACGCAAGAGCTATTTGGTT
GGTTACAAACTCTCTGATGCAATGAGAATCGGAACGGAACATTCAGTGCT
GCTGATACATGAATGAATGAATGAATGAATGATGGAATGATGATGATGAT
GAAGAATAATGCAAGCAATAAAATTGAATTCATATATAAATGCCAGGCGA
GGAGCGCTGACATTCCCACGACTGTCGAGCACTGCGGATATTGCCACATG
TCACTGAAGAATGCAAGCGATGCGATAGCTCACTACCAGACTCAGAAACA
CGCATTGAACATGACAAACCGCTCTAGAAACTATGAATTATGGTGCGGTA
TCTGTCAGATATCATTCACTAATCAGAATTTTCTCGATTTACATTTGGCA
GGATTCAAGCATTTTGTGCGCTTGAACCGTGGCAACCAAGCTCCTGAAGG
AGCGTTCGGTGAGAGATTGATAAAGATGCGGGCAAAGCTTCAAAATTTGA
AACAGAGTAGGAAAGCAAAAAAATCGAGTAATCTGGAGAACTGCCAAATT
CTGTCCAATGAACAGTCGCAAAATTAGCTGAATCTCCAATGGTTGCGATT
CATCATGATCTTATTATTATTATTATTATTAATCACCACTGGCATTAAAT
ATGCGTTTTCTGCTGCTAATGTTCCTTGAGTTTCCTTAGTGGTTGATTGA
CATCGATTATCGTATTTTCTAAAATGGAATAAAACGTATTGATTTTTGAT
GTGCAATTC
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protein sequence of SMED30003533-orf-1

>SMED30003533-orf-1 ID=SMED30003533-orf-1|Name=SMED30003533-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MNDGMMMMMKNNASNKIEFIYKCQARSADIPTTVEHCGYCHMSLKNASDA
IAHYQTQKHALNMTNRSRNYELWCGICQISFTNQNFLDLHLAGFKHFVRL
NRGNQAPEGAFGERLIKMRAKLQNLKQSRKAKKSSNLENCQILSNEQSQN
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR013087Znf_C2H2_type
IPR036236Znf_C2H2_sf
IPR003604Matrin/U1-like-C_Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0003676nucleic acid binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePFAMPF12874zf-metcoord: 32..55
e-value: 2.6E-5
score: 24.5
NoneNo IPR availableGENE3DG3DSA:3.30.160.60coord: 19..64
e-value: 3.4E-7
score: 31.7
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 33..55
IPR036236Zinc finger C2H2 superfamilySUPERFAMILYSSF57667beta-beta-alpha zinc fingerscoord: 30..59