SMED30005997

Overview
NameSMED30005997
Smed IDSMED30005997
Length (bp)705
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 SMED30005997 (SMED30005997) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30005997 (SMED30005997) 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 SMED30005997 (SMED30005997) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30005997 (SMED30005997) 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



SMED30005997

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
X1 cellSMED30005997SMESG000050405.1 SmedASXL_009520SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
pharynxSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30005997SMESG000050405.1 dd_Smed_v4_1663_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30005997SMESG000050405.1 dd_Smed_v6_1663_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30005997 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003449:14424..15264 +3401
v31.003856:27018..27858 -3374
Homology
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BLAST of SMED30005997 vs. Ensembl Sea Lamprey
Match: rbm4.2 (RNA binding motif protein 4.2 [Source:ZFIN;Acc:ZDB-GENE-030131-3019])

HSP 1 Score: 46.595 bits (109), Expect = 1.059e-6
Identity = 21/67 (31.34%), Postives = 34/67 (50.75%), Query Frame = 1 
Query:   82 NLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVEL 282
             + V  + P  T+ +L   F+ FGPV +  +++D  +VHM   DD    +  +      GRRI V+L
Sbjct:   79 KMYVGNVTPDCTNVELRAKFEEFGPVAECDIVKDYAFVHMEREDDARAAIRALDGSEFKGRRILVQL 145
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BLAST of SMED30005997 vs. Ensembl Sea Lamprey
Match: syncripl (synaptotagmin binding, cytoplasmic RNA interacting protein, like [Source:ZFIN;Acc:ZDB-GENE-030131-3104])

HSP 1 Score: 45.4394 bits (106), Expect = 5.303e-6
Identity = 21/70 (30.00%), Postives = 37/70 (52.86%), Query Frame = 1 
Query:   73 QVMNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVEL 282
            +V  L V+ +  + T   L D F VFG +E+   ++D  +VH  +RDD +K ++ M    + G  + + L
Sbjct:  344 KVKVLFVRNLASAVTEEILQDTFSVFGKLERVKKLKDYAFVHFEDRDDAVKAMDEMNGKPLEGEPLVIVL 413
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BLAST of SMED30005997 vs. Planmine SMEST
Match: SMESG000050405.1 (SMESG000050405.1)

HSP 1 Score: 365.925 bits (938), Expect = 1.673e-130
Identity = 178/179 (99.44%), Postives = 178/179 (99.44%), Query Frame = 1 
Query:   79 MNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP 615
            MNLIVQGIPP TTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP
Sbjct:    1 MNLIVQGIPPLTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKILNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRDVGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDPHGYSRDPTMRPAPEYYYRIKLLDSKSKHP 179
The following BLAST results are available for this feature:
BLAST of SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 2
Match NameE-valueIdentityDescription
rbm4.21.059e-631.34RNA binding motif protein 4.2 [Source:ZFIN;Acc:ZDB... [more]
syncripl5.303e-630.00synaptotagmin binding, cytoplasmic RNA interacting... [more]
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BLAST of SMED30005997 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 SMED30005997 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 SMED30005997 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 SMED30005997 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000050405.11.673e-13099.44SMESG000050405.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005997 ID=SMED30005997|Name=SMED30005997|organism=Schmidtea mediterranea sexual|type=transcript|length=705bp
AGTAGGAAAGTGCGGATTTTTTGACTTTAATATTTTTTACTTCAATCTTT
ATTTTAAATATTTATTTGATAGCAAGTTATGAATCTTATAGTTCAAGGAA
TTCCCCCATCAACTACTTCATATGATTTAACTGATTATTTTAAAGTATTT
GGACCGGTTGAGAAGGCATATGTTATGGAAGATGTTGGATATGTGCATAT
GATTAATCGAGATGATGGAATTAAGATATTAAATACTATGAGAAACCTTT
ATATGTCAGGTAGACGAATCTTTGTCGAACTTGATAGTGGTATGGGAATG
AATAGAGAGAGAGAACAAATGCCATATCATGAACCAATGCCTAATCCTTA
CAGTGGATGGACCGAAATACCAAGAGATGTAGGTCATTCTTATGATTACG
GAATGCCACAGGAAAGGTTTTCCAAAACTGATGTAGATCCATGGAAGCAA
GTTATTCCTGAACAAAATTTAAACGGATCCCGATCTGATGAAAGATTAAT
TACTGAATCGTATGTATATGTTGATCCGCACGGATACTCTCGAGATCCAA
CCATGCGTCCAGCACCGGAATATTATTACAGAATTAAACTTCTCGATTCT
AAGTCGAAACACCCTTGAAATTATTTACACTGTTGTGAATATATGTATTT
GTTTTGGTCTAAATTTTAAAATAATATTTGGTATTACAGATTTTGTAGAG
TTGCG
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protein sequence of SMED30005997-orf-1

>SMED30005997-orf-1 ID=SMED30005997-orf-1|Name=SMED30005997-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp
MNLIVQGIPPSTTSYDLTDYFKVFGPVEKAYVMEDVGYVHMINRDDGIKI
LNTMRNLYMSGRRIFVELDSGMGMNREREQMPYHEPMPNPYSGWTEIPRD
VGHSYDYGMPQERFSKTDVDPWKQVIPEQNLNGSRSDERLITESYVYVDP
HGYSRDPTMRPAPEYYYRIKLLDSKSKHP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR035979RBD_domain_sf
IPR000504RRM_dom
IPR012677Nucleotide-bd_a/b_plait_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0000166nucleotide binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000504RNA recognition motif domainSMARTSM00360rrm1_1coord: 2..67
e-value: 2.4E-11
score: 53.7
IPR000504RNA recognition motif domainPFAMPF00076RRM_1coord: 3..64
e-value: 5.0E-7
score: 29.4
IPR000504RNA recognition motif domainPROSITEPS50102RRMcoord: 1..71
score: 11.179
IPR012677Nucleotide-binding alpha-beta plait domain superfamilyGENE3DG3DSA:3.30.70.330coord: 1..69
e-value: 4.1E-11
score: 44.9
NoneNo IPR availableCDDcd00590RRM_SFcoord: 3..67
e-value: 1.34255E-11
score: 55.3889
IPR035979RNA-binding domain superfamilySUPERFAMILYSSF54928RNA-binding domain, RBDcoord: 2..92