SMED30007916

Overview
NameSMED30007916
Smed IDSMED30007916
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 SMED30007916 (SMED30007916) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007916 (SMED30007916) 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 SMED30007916 (SMED30007916) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007916 (SMED30007916) 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



SMED30007916

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007916h1SMcG0020978 SmedASXL_008803SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30007916h1SMcG0020978 SmedASXL_008803SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30007916h1SMcG0020978 dd_Smed_v4_11930_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30007916h1SMcG0020978 dd_Smed_v4_11930_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
SMED30007916 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007135:9489..13866 +6529
Homology
[Close]
BLAST of SMED30007916 vs. Planmine SMEST
Match: SMESG000016771.1 (SMESG000016771.1)

HSP 1 Score: 721.465 bits (1861), Expect = 0.000e+0
Identity = 382/386 (98.96%), Postives = 384/386 (99.48%), Query Frame = 1 
Query:   55 MSDLEMHINSSLCDESNTISLNSVNNPAILKPINLIKNEDSIDNSQSDEKKHKLIKEIDDCSLDISSVNSRTRFRKSLVDDEKKNNNANYPCHSKNNLPPNNHDNTTRSTFLXXXXXXXXXXXXFEDSPIKPNKNSSHNVNSLISSTCLYDSQNKVENINADRTDEDDRNAKKSNKLSFICSTCPEEFETAYQLKTHVFLHRYESQNFENASSPTTESESLNGNAXXXXXXXXXXXXIKRRNTKRKKPDVDDDNEEKVSKIPKRILTCDLCPKVFHRPENLTVHRNKYHNIKKNTEKISNTPKPKTVKASKCQQCSMEFESLNILQIHQTAYCFKAAPDLKEWVSKNMSYHFGCVVCGLSFKSSKRLEFHKEEHADFKWPTKKPSS 1212
            MSDLEMHINSSLCDESNTISLNSVNNPAILKPINLIKNEDSIDNSQSDEKKHKLIKEIDDCSLDISSVNSRTRFRKSLVDDEKKNNNANYPCHSKNNLPPNNHDNT+RS+FLNKNGNINNKENNFEDSPIKPNKN  HNVNSLISSTCLYDSQNKVENINADRTDEDDRNAKKSNKLSFICSTCPEEFETAYQLKTHVFLHRYESQNFENASSPTTESESLNGNASSSETLSTRNSSIKRRNTKRKKPDVDDDNEEKVSKIPKRILTCDLCPKVFHRPENLTVHRNKYHNIKKNTEKISNTPKPKTVKASKCQQCSMEFESLNILQIHQTAYCFKAAPDLKEWVSKNMSYHFGCVVCGLSFKSSKRLEFHKEEHADFKWPTKKPSS
Sbjct:    1 MSDLEMHINSSLCDESNTISLNSVNNPAILKPINLIKNEDSIDNSQSDEKKHKLIKEIDDCSLDISSVNSRTRFRKSLVDDEKKNNNANYPCHSKNNLPPNNHDNTSRSSFLNKNGNINNKENNFEDSPIKPNKNCFHNVNSLISSTCLYDSQNKVENINADRTDEDDRNAKKSNKLSFICSTCPEEFETAYQLKTHVFLHRYESQNFENASSPTTESESLNGNASSSETLSTRNSSIKRRNTKRKKPDVDDDNEEKVSKIPKRILTCDLCPKVFHRPENLTVHRNKYHNIKKNTEKISNTPKPKTVKASKCQQCSMEFESLNILQIHQTAYCFKAAPDLKEWVSKNMSYHFGCVVCGLSFKSSKRLEFHKEEHADFKWPTKKPSS 386
The following BLAST results are available for this feature:
BLAST of SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 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 SMED30007916 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000016771.10.000e+098.96SMESG000016771.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007916 ID=SMED30007916|Name=SMED30007916|organism=Schmidtea mediterranea sexual|type=transcript|length=1329bp
AATTAACGAATAAAATATTTCAAAAATTAAATTAAATTCTAAAATTTCCA
ATCTATGAGTGATTTAGAAATGCATATCAACAGTTCTTTATGTGATGAAT
CTAATACGATATCTTTGAATTCAGTGAACAATCCTGCAATATTAAAACCT
ATTAATCTAATTAAAAATGAAGACTCTATTGATAACAGTCAATCAGACGA
AAAAAAGCATAAATTAATAAAAGAAATCGACGATTGTAGTTTGGATATAT
CTTCAGTTAATTCAAGAACTAGATTTCGAAAATCATTAGTAGATGATGAA
AAAAAGAATAATAATGCAAATTATCCATGTCATTCAAAGAATAATTTACC
TCCTAACAACCACGATAACACAACTCGTTCGACTTTCTTAAATAAAAATG
GTAATATTAATAATAAAGAAAATAATTTTGAGGATTCTCCTATTAAACCC
AACAAAAATAGCTCCCATAACGTTAATTCGCTAATTTCTTCAACGTGTCT
TTATGATTCACAAAATAAAGTCGAAAATATAAACGCTGATCGCACGGACG
AAGACGATAGAAATGCTAAAAAATCCAATAAGTTATCATTTATCTGTTCA
ACATGTCCCGAAGAATTCGAAACTGCTTATCAATTGAAAACACATGTATT
TCTACATCGTTACGAATCTCAAAATTTTGAGAATGCTTCTTCACCAACAA
CCGAATCGGAATCTCTGAATGGCAATGCTAGCTCGTCTGAGACTTTATCA
ACACGAAATTCATCAATTAAAAGAAGAAACACGAAAAGAAAGAAACCAGA
TGTTGATGATGATAATGAAGAAAAAGTTTCGAAAATTCCCAAAAGGATTT
TAACATGTGATTTATGTCCTAAAGTTTTCCATCGTCCCGAAAATCTTACT
GTTCACAGAAATAAATATCACAATATAAAAAAAAACACGGAAAAAATATC
GAATACACCCAAACCGAAAACTGTGAAGGCTTCCAAGTGTCAACAGTGTT
CGATGGAATTCGAAAGCTTGAACATCCTTCAGATCCACCAAACAGCCTAT
TGTTTCAAAGCAGCCCCTGATCTTAAAGAATGGGTATCGAAAAACATGTC
CTATCATTTCGGTTGCGTTGTTTGCGGTCTGTCATTCAAATCATCAAAAC
GCCTCGAGTTTCACAAAGAAGAACACGCAGATTTTAAATGGCCCACCAAA
AAACCCTCCAGCTAGTTTGATTTCGAATGATAGATGTGTTATTGAAATTT
GTAATTTGTGTTGCAATAAAATATAATTATTTGTGATTTTTCAATTTTGT
GTTCTATTTTGTTATGTTACTTTTTGTTG
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protein sequence of SMED30007916-orf-1

>SMED30007916-orf-1 ID=SMED30007916-orf-1|Name=SMED30007916-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=387bp
MSDLEMHINSSLCDESNTISLNSVNNPAILKPINLIKNEDSIDNSQSDEK
KHKLIKEIDDCSLDISSVNSRTRFRKSLVDDEKKNNNANYPCHSKNNLPP
NNHDNTTRSTFLNKNGNINNKENNFEDSPIKPNKNSSHNVNSLISSTCLY
DSQNKVENINADRTDEDDRNAKKSNKLSFICSTCPEEFETAYQLKTHVFL
HRYESQNFENASSPTTESESLNGNASSSETLSTRNSSIKRRNTKRKKPDV
DDDNEEKVSKIPKRILTCDLCPKVFHRPENLTVHRNKYHNIKKNTEKISN
TPKPKTVKASKCQQCSMEFESLNILQIHQTAYCFKAAPDLKEWVSKNMSY
HFGCVVCGLSFKSSKRLEFHKEEHADFKWPTKKPSS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR013087Znf_C2H2_type
IPR036236Znf_C2H2_sf
IPR015880Znf_C2H2-like
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding
GO:0003676nucleic acid binding
GO:0008270zinc ion binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR013087Zinc finger C2H2-typeSMARTSM00355c2h2final6coord: 310..330
e-value: 180.0
score: 2.1
coord: 179..201
e-value: 0.046
score: 22.9
coord: 266..289
e-value: 0.048
score: 22.8
coord: 352..374
e-value: 2.4
score: 17.1
IPR013087Zinc finger C2H2-typePFAMPF00096zf-C2H2coord: 267..289
e-value: 2.7E-4
score: 21.2
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 181..201
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 268..289
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 354..374
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 179..206
score: 9.556
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 352..379
score: 9.328
IPR013087Zinc finger C2H2-typePROSITEPS50157ZINC_FINGER_C2H2_2coord: 266..294
score: 10.055
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 208..237
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 89..103
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 208..256
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 76..103
NoneNo IPR availablePANTHERPTHR24390:SF81ZINC FINGER PROTEIN 711coord: 48..374
NoneNo IPR availablePANTHERPTHR24390FAMILY NOT NAMEDcoord: 48..374
IPR036236Zinc finger C2H2 superfamilySUPERFAMILYSSF57667beta-beta-alpha zinc fingerscoord: 179..285