SMED30033143

Overview
NameSMED30033143
Smed IDSMED30033143
Length (bp)2061
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 SMED30033143 (SMED30033143) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30033143 (SMED30033143) 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 SMED30033143 (SMED30033143) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30033143 (SMED30033143) 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




SMED30033143

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30033143SMESG000071759.1 SmedASXL_019257SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30033143SMESG000071759.1 SmedASXL_004304SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
reproductive organSMED30033143SMESG000071759.1 Contig38146newmark_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30033143SMESG000071759.1 Contig38146uc_Smed_v2PMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite RNA-sequencing evidence
testisSMED30033143SMESG000071759.1 PL06007B2H07ncbi_smed_estsPMID:28434803
Rouhana et al., 2017
whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testis primordiumSMED30033143SMESG000071759.1 Contig4147_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
neoblastSMED30033143SMESG000071759.1 SMED_06860_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30033143SMESG000071759.1 SMED_06860_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30033143 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009267:2871..14405 +7040
Homology
BLAST of SMED30033143 vs. Planmine SMEST
Match: SMESG000071759.1 (SMESG000071759.1)

HSP 1 Score: 798.89 bits (2062), Expect = 0.000e+0
Identity = 401/438 (91.55%), Postives = 406/438 (92.69%), Query Frame = 2
Query:  158 MPISLPVNYSNKFNQGQGIVNTTIRIPDKKPINECRKIRNNVRSDDATLTFEYNKDVDCIQKLLSKYEGKSCSPKKEVISNPTTSIKINFAAFDFPECQSKLGSEPWKYVPRRERKNYQNNDKRAIVKESRKFKKPSDNIQKGKNVLESSKIGQVESKKFGEMKIIQKQEAEFLKSQYDKDKRNLGHLKNEEGKPNIQSVVTPENNRNGEISQSRLNEYTEGNVDYHLKDNQIFIRDADGKLIQKGNPNLEFNVYPESIEMSAGMVNNEFVTSDYNGTKMENGLYSEFSPYNSDETQESGGFAKLKNSAENGERIIEENFVPFFESKHHQKTFEKGRQKPNLTDTSEKFIYDIFETVSSNQFEEENYHQISSDNMRSSDKFVYDIFETVHMNRFEEENYDQITSDNVELRRNNEICKKQDFIEAGEKFVYDIFETVPM 1471
            MPISLPVNYSNKFNQGQGIVNTTIRIPDKKPINECRKIRNNVR              +CIQKLLSKYEGKSCSPKKEVISNPTTSIKINFAAFDFPECQSKLGSEPWKYVPRRERKNYQNNDKRAIVKESRKFKKPSDNIQKGKNVLESSKIGQVESKKFGEMKIIQKQEAEFLKSQYDKDKRNLGHLKNEEGKPNIQSVVTPENNRNGEISQSRLNEYTEGNVDYHLKDNQIFIRDADGKLIQK              EMSAGMVNNEFVTSDYNGTKMENGLYSEFSPYNSDETQESGGFAKLKNSAENGERIIEENFVPFFESKHHQKTFEKGRQKPNLTDTSEKFIYDIFETVSSNQFEEENYHQISSDNMRSSDKFVYDIFETVH+NR EEENYDQ+TSDNVELR+NNEI KKQDFIE GEKFV+DIFETV M
Sbjct:    1 MPISLPVNYSNKFNQGQGIVNTTIRIPDKKPINECRKIRNNVR--------------NCIQKLLSKYEGKSCSPKKEVISNPTTSIKINFAAFDFPECQSKLGSEPWKYVPRRERKNYQNNDKRAIVKESRKFKKPSDNIQKGKNVLESSKIGQVESKKFGEMKIIQKQEAEFLKSQYDKDKRNLGHLKNEEGKPNIQSVVTPENNRNGEISQSRLNEYTEGNVDYHLKDNQIFIRDADGKLIQK--------------EMSAGMVNNEFVTSDYNGTKMENGLYSEFSPYNSDETQESGGFAKLKNSAENGERIIEENFVPFFESKHHQKTFEKGRQKPNLTDTSEKFIYDIFETVSSNQFEEENYHQISSDNMRSSDKFVYDIFETVHLNRVEEENYDQMTSDNVELRKNNEIRKKQDFIEGGEKFVFDIFETVHM 410          

HSP 2 Score: 498.434 bits (1282), Expect = 2.413e-168
Identity = 244/280 (87.14%), Postives = 254/280 (90.71%), Query Frame = 2
Query: 1166 RQKPNLTDTSEKFIYDIFETVSSNQFEEENYHQISSDN---------------MRSSDKFVYDIFETVHMNRFEEENYDQITSDNVELRRNNEICKKQDFIEAGEKFVYDIFETVPMAMAKYFKEYAEQNPMGTSKNVYGDLGYLTDDNTEGSTNPFIFIYNSGSDYDKIEQSHRPIDGTFNQQIYKVSNAPNLLTATNPDNASLFNRVPNSINKNTNPNLNPTVRKSQRIDFKAADPFSFIDLKNRKKSNEPIRFVLPPNFCQASLSKTASADLSNKTK 1960
            R+K +  +  EKF++DIFETV  N+FEEENY Q++SDN               +   +KFVYDIFETVHMNRFEEENYDQITSDNVELRRNNEICKKQDFIEAGEKFVYDIFETVPMAMAKYFKEYAEQNPMGTSKNVYGDLGYLTDDNTEGSTNPFIFIYNSGSDYDKIEQSHRPIDGTFNQQIYKVSNAPNLLTATNPDNASLFNRVPNSINKNTNPNLNPTVRKSQRIDFKAADPFSFIDLKNRKKSNEPIRFVLPPNFCQASLSKTASADLSNKTK
Sbjct:  388 RKKQDFIEGGEKFVFDIFETVHMNRFEEENYDQMTSDNVELRKNNEIRKKQDFIEGGEKFVYDIFETVHMNRFEEENYDQITSDNVELRRNNEICKKQDFIEAGEKFVYDIFETVPMAMAKYFKEYAEQNPMGTSKNVYGDLGYLTDDNTEGSTNPFIFIYNSGSDYDKIEQSHRPIDGTFNQQIYKVSNAPNLLTATNPDNASLFNRVPNSINKNTNPNLNPTVRKSQRIDFKAADPFSFIDLKNRKKSNEPIRFVLPPNFCQASLSKTASADLSNKTK 667          
The following BLAST results are available for this feature:
BLAST of SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 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 SMED30033143 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000071759.12.413e-16891.55SMESG000071759.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30033143 ID=SMED30033143|Name=SMED30033143|organism=Schmidtea mediterranea sexual|type=transcript|length=2061bp
CTAAAATTAAATTACTAATTTGGGCTCTTTTATTTTGATTTTACATTATA
AAATTTATAAAAAACCAACAAAATTTTAAAATTTGTTAAATTCATGTAAT
CGTTTGGTTTCATTTTTAAGTTTGATTTAAAGTGAAGTTATTGTTAAATA
ATAAACCATGCCTATTTCATTACCTGTAAATTATTCCAACAAATTCAATC
AAGGGCAAGGCATAGTAAATACGACTATTCGAATCCCAGATAAGAAACCG
ATAAATGAATGCAGGAAAATTCGAAATAATGTTAGAAGTGACGATGCAAC
GCTTACTTTCGAATATAATAAAGATGTAGATTGTATTCAAAAATTACTAT
CGAAATATGAAGGAAAAAGTTGTTCACCGAAGAAAGAAGTTATAAGTAAC
CCAACGACGTCGATTAAGATAAATTTCGCTGCTTTTGATTTTCCAGAATG
TCAATCAAAGTTAGGAAGCGAACCATGGAAATATGTTCCAAGAAGAGAGA
GGAAAAACTACCAGAATAATGATAAAAGAGCCATAGTAAAAGAGTCCAGA
AAATTCAAAAAACCATCAGACAATATTCAAAAAGGTAAAAATGTATTAGA
AAGTTCGAAAATTGGCCAGGTAGAAAGTAAAAAATTTGGGGAAATGAAAA
TTATTCAGAAACAAGAAGCCGAATTTTTAAAAAGTCAATATGATAAAGAT
AAACGGAATTTGGGTCATCTCAAAAATGAGGAAGGAAAACCCAACATTCA
ATCTGTTGTTACACCTGAAAATAATCGAAATGGAGAAATTTCACAATCAC
GATTGAATGAATATACAGAAGGAAATGTTGATTATCACTTGAAAGATAAT
CAAATTTTTATCAGAGATGCAGATGGAAAATTAATACAGAAAGGTAATCC
AAATTTAGAGTTCAATGTATATCCTGAAAGTATAGAAATGTCAGCAGGAA
TGGTTAATAATGAATTTGTAACTAGTGATTATAATGGAACCAAGATGGAA
AATGGTCTATATTCAGAGTTTTCTCCTTATAATAGTGATGAAACTCAAGA
ATCAGGAGGATTTGCAAAATTAAAAAATAGCGCAGAAAACGGAGAAAGAA
TAATTGAGGAAAACTTTGTTCCATTTTTTGAAAGTAAGCATCATCAAAAG
ACTTTCGAAAAGGGTCGACAGAAACCAAATTTAACCGATACCAGTGAAAA
ATTTATTTACGATATCTTTGAAACCGTTAGTTCAAATCAGTTTGAAGAGG
AGAATTATCATCAAATATCCTCCGATAATATGAGATCAAGTGATAAATTT
GTGTACGATATTTTTGAAACCGTCCATATGAATCGGTTTGAAGAGGAGAA
TTATGATCAAATTACTTCCGACAATGTCGAATTAAGAAGGAATAATGAAA
TTTGTAAAAAACAGGATTTCATTGAAGCAGGCGAAAAATTTGTTTACGAT
ATTTTTGAAACGGTTCCTATGGCTATGGCTAAATATTTTAAAGAATATGC
TGAACAAAATCCAATGGGGACCTCTAAAAATGTATATGGGGATTTGGGTT
ATTTAACAGACGATAATACAGAAGGAAGCACTAATCCGTTTATTTTCATC
TATAACTCAGGTTCAGATTATGATAAAATTGAACAGAGCCATAGACCAAT
AGATGGAACGTTTAATCAACAAATTTATAAAGTCTCCAATGCTCCTAACT
TACTAACAGCGACAAATCCGGACAATGCAAGCTTATTCAATCGTGTACCA
AATTCTATCAATAAAAATACAAATCCAAACCTGAATCCAACAGTTCGAAA
AAGCCAGCGAATCGATTTTAAAGCAGCTGATCCGTTCAGTTTTATCGATT
TAAAAAACCGCAAAAAGTCTAATGAACCGATTAGATTTGTGCTTCCACCA
AATTTTTGTCAGGCGAGCTTATCAAAAACTGCTTCGGCGGATTTATCAAA
TAAAACAAAATGAAAAGTTCCCTACAATTATTCCAAAAGTCAGCCACATT
CATCTAACTCTGATTCTTTATTTCGAAATTTGATTTAAATAAAATAACAT
ATTGTGTAAAT
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protein sequence of SMED30033143-orf-1

>SMED30033143-orf-1 ID=SMED30033143-orf-1|Name=SMED30033143-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=602bp
MPISLPVNYSNKFNQGQGIVNTTIRIPDKKPINECRKIRNNVRSDDATLT
FEYNKDVDCIQKLLSKYEGKSCSPKKEVISNPTTSIKINFAAFDFPECQS
KLGSEPWKYVPRRERKNYQNNDKRAIVKESRKFKKPSDNIQKGKNVLESS
KIGQVESKKFGEMKIIQKQEAEFLKSQYDKDKRNLGHLKNEEGKPNIQSV
VTPENNRNGEISQSRLNEYTEGNVDYHLKDNQIFIRDADGKLIQKGNPNL
EFNVYPESIEMSAGMVNNEFVTSDYNGTKMENGLYSEFSPYNSDETQESG
GFAKLKNSAENGERIIEENFVPFFESKHHQKTFEKGRQKPNLTDTSEKFI
YDIFETVSSNQFEEENYHQISSDNMRSSDKFVYDIFETVHMNRFEEENYD
QITSDNVELRRNNEICKKQDFIEAGEKFVYDIFETVPMAMAKYFKEYAEQ
NPMGTSKNVYGDLGYLTDDNTEGSTNPFIFIYNSGSDYDKIEQSHRPIDG
TFNQQIYKVSNAPNLLTATNPDNASLFNRVPNSINKNTNPNLNPTVRKSQ
RIDFKAADPFSFIDLKNRKKSNEPIRFVLPPNFCQASLSKTASADLSNKT
K*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
PLANA:0000429neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
PLANA:0003304testis primordium
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 392..412
NoneNo IPR availableCOILSCoilCoilcoord: 171..191
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 195..210
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 185..210