SMED30034441

Overview
NameSMED30034441
Smed IDSMED30034441
Length (bp)1522
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 SMED30034441 (SMED30034441) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034441 (SMED30034441) 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 SMED30034441 (SMED30034441) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034441 (SMED30034441) 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



SMED30034441

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
nervous systemSMED30034441h1SMcG0000837 dd_Smed_v4_12592_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034441h1SMcG0000837 dd_Smed_v4_12740_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034441h1SMcG0000837 dd_Smed_v4_12740_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034441h1SMcG0000837 dd_Smed_v4_12740_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30034441 vs. Planmine SMEST
Match: SMESG000039018.1 (SMESG000039018.1)

HSP 1 Score: 250.751 bits (639), Expect = 7.300e-79
Identity = 117/129 (90.70%), Postives = 123/129 (95.35%), Query Frame = 3 
Query:  147 GKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRLSWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVVRARQYLANIEEDIATGRIANTYSHPPPCNSTLNYTGGRT 533
            GKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSR ESRRLSWQSG+ NR+SWLPDQ+ E+WSPVW+IREHARHLL RLESHQRQVDLHVVRA QYLANI+EDIA GRIANTYSHPPPCNSTLNYTGGRT
Sbjct:  183 GKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRPESRRLSWQSGKRNRDSWLPDQQWEEWSPVWDIREHARHLLSRLESHQRQVDLHVVRAGQYLANIQEDIAAGRIANTYSHPPPCNSTLNYTGGRT 311

HSP 2 Score: 49.2914 bits (116), Expect = 4.404e-6
Identity = 20/23 (86.96%), Postives = 22/23 (95.65%), Query Frame = 1 
Query:  526 EEPVMVFSNCSPEEWMERGFTDL 594
            + PVMVFSNCSPEEW+ERGFTDL
Sbjct:  330 KRPVMVFSNCSPEEWVERGFTDL 352
[Close]
BLAST of SMED30034441 vs. Planmine SMEST
Match: SMESG000039018.1 (SMESG000039018.1)

HSP 1 Score: 247.669 bits (631), Expect = 3.508e-78
Identity = 116/128 (90.62%), Postives = 122/128 (95.31%), Query Frame = 3 
Query:  150 KSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRLSWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVVRARQYLANIEEDIATGRIANTYSHPPPCNSTLNYTGGRT 533
            KSGPLIYVPTHVADRWRQAWRRFGQERCPEFSR ESRRLSWQSG+ NR+SWLPDQ+ E+WSPVW+IREHARHLL RLESHQRQVDLHVVRA QYLANI+EDIA GRIANTYSHPPPCNSTLNYTGGRT
Sbjct:  136 KSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRPESRRLSWQSGKRNRDSWLPDQQWEEWSPVWDIREHARHLLSRLESHQRQVDLHVVRAGQYLANIQEDIAAGRIANTYSHPPPCNSTLNYTGGRT 263

HSP 2 Score: 49.2914 bits (116), Expect = 3.858e-6
Identity = 20/23 (86.96%), Postives = 22/23 (95.65%), Query Frame = 1 
Query:  526 EEPVMVFSNCSPEEWMERGFTDL 594
            + PVMVFSNCSPEEW+ERGFTDL
Sbjct:  282 KRPVMVFSNCSPEEWVERGFTDL 304
[Close]
BLAST of SMED30034441 vs. Planmine SMEST
Match: SMESG000071716.1 (SMESG000071716.1)

HSP 1 Score: 222.631 bits (566), Expect = 7.928e-76
Identity = 132/286 (46.15%), Postives = 162/286 (56.64%), Query Frame = 3 
Query:  144 SGKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRLSWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVVRARQYLANIEEDIATGRIANTYSHPPPCNSTLNYTGGRTRNGVLKLFSGRMDGERFYGPLIPLFHSRGRPNLTHHN*YG*IFCLNK*LATLDAHFVLFGCFSKTFFHLCLIVFILNNSGLVTNNLMSLIIAMESLQILRI*LVRAQQTNKTLYNQIIQLTREIHQTKATWVDPTKIKSIHQRLTAAQKGWADESK 1001
            +G S P + +P  + DRWR+AWR+F Q RC EF   E R+ + Q    NR     +Q  E+ +P  EI+EHAR LL  L +HQRQVDL VVRARQ LANIEEDI TGR A  Y HP                                              L+    +G   C N+ +  L  +FVLFG  +     LCLI  +L NS  +   LMSLI  M+SLQ+L+  L RAQQ NKTLY+QIIQLTRE+HQT+ATWVDP KIK +HQRLTAAQKGWA+E +
Sbjct:   29 TGCSDPDL-IPIQLTDRWREAWRQFRQARCLEFPPLEPRQNNGQPESYNRNPEASEQLWEECNPAQEIQEHARRLLDSLLNHQRQVDLQVVRARQCLANIEEDIETGRNAAAYHHP----------------------------------------------LSRRPIHG---CTNEEMVLLAINFVLFGVITICQRSLCLIPVMLINSVTIVTLLMSLIPEMDSLQLLQTELARAQQNNKTLYDQIIQLTREVHQTRATWVDPAKIKPLHQRLTAAQKGWAEEKQ 264

HSP 2 Score: 81.6481 bits (200), Expect = 7.928e-76
Identity = 48/67 (71.64%), Postives = 54/67 (80.60%), Query Frame = 1 
Query:  982 DGQTNQSLRTQIRGLEVALSACQEGAAVTYPFVFAPS*LAYRESVXXXXXXXXXXXXITNSYRPGVK 1182
            + Q NQSLRTQIRGL+VAL A QEGAAVTYP VFAP+ LAYRESV TPA+A+TP    T +YRPG K
Sbjct:  262 EKQMNQSLRTQIRGLDVALLASQEGAAVTYPLVFAPAQLAYRESVTTPASASTPVATATTNYRPGRK 328
[Close]
BLAST of SMED30034441 vs. Planmine SMEST
Match: SMESG000014158.1 (SMESG000014158.1)

HSP 1 Score: 213.386 bits (542), Expect = 1.747e-65
Identity = 96/130 (73.85%), Postives = 112/130 (86.15%), Query Frame = 3 
Query:  150 KSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRLSWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVVRARQYLANIEEDIATGRIANTYSHPPPCNSTLNYTGGRTRN 539
            KSGP++YVP+HVADRWRQAWR+F Q+RCPE SR ESR+LSWQSGESN   WL DQ+ E+WSP WEIREHARHLLGRLE+HQRQVD+ V+R+RQYLANIEEDI+ GRIAN Y HPP   + LNYTGG+T +
Sbjct:  104 KSGPMVYVPSHVADRWRQAWRQFSQDRCPELSRPESRQLSWQSGESNHNPWLSDQQWEEWSPAWEIREHARHLLGRLENHQRQVDVQVIRSRQYLANIEEDISAGRIANVYCHPPQDKAPLNYTGGKTND 233
[Close]
BLAST of SMED30034441 vs. Planmine SMEST
Match: SMESG000058084.1 (SMESG000058084.1)

HSP 1 Score: 213.001 bits (541), Expect = 2.695e-64
Identity = 134/312 (42.95%), Postives = 172/312 (55.13%), Query Frame = 3 
Query:  129 SNQSYSGKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRLSWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVVRARQYLANIEEDIATGRIANTYSHPP---PCNSTLNYTGGRTRNGVLKLFSGRMDGERFYGPLIPLFHSRGRPNLTHHN*YG*IFCLNK*LATLDAHFVLFGCFSKTFFHLCLIVFILNNSGLVTNNLMSLIIAMESLQILRI*LVRAQQTNKTLYNQIIQLTREIHQTKATWVDPTKIKSIHQRLTAAQKGWADESKPPNT-DTGVGGCPVRLSG 1052
            S+    G+S P + +P  + DRWR+AW++F Q RC EFS  ESR++S Q  + NR     +Q  E+W+P  EI EHAR LL  L +HQRQVDL VVRARQ LANIE+DI TGRIA  Y HP    P     N   G  R       + R+   +             RP                   T+ ++       ++ F  +      L  S ++   LMSLI  M+SLQ+LR  L  AQQ NKTLY+QII+LTRE+HQT+ATWVDP KIK +HQRLTAAQKGWA+E +   +  T + G  V LS 
Sbjct:   25 SDPQIIGRSDPDL-IPIQLPDRWREAWKQFRQARCLEFSPLESRQISGQPEDFNRNPEASEQLLEEWNPAQEIHEHARRLLDSLLNHQRQVDLQVVRARQCLANIEDDIETGRIAAAYRHPLSRRPMYGCTNEEMGENRKDSQVARTNRVRNTK-------------RP------------------VTIFSNCSPEEWVARGFTDILCWYLELTCSVIIVTLLMSLIPEMDSLQLLRTELALAQQNNKTLYDQIIELTREVHQTRATWVDPAKIKPLHQRLTAAQKGWAEEKQINQSLRTQIRGLEVALSA 304

HSP 2 Score: 85.5001 bits (210), Expect = 7.137e-18
Identity = 50/67 (74.63%), Postives = 55/67 (82.09%), Query Frame = 1 
Query:  982 DGQTNQSLRTQIRGLEVALSACQEGAAVTYPFVFAPS*LAYRESVXXXXXXXXXXXXITNSYRPGVK 1182
            + Q NQSLRTQIRGLEVALSA QEGAAVTYP VFAP+ LAYRESV TPA+A+TP    T +YRPG K
Sbjct:  284 EKQINQSLRTQIRGLEVALSASQEGAAVTYPLVFAPAQLAYRESVTTPASASTPVATATTNYRPGRK 350
The following BLAST results are available for this feature:
BLAST of SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 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 SMED30034441 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000039018.17.300e-7990.70SMESG000039018.1[more]
SMESG000039018.13.508e-7890.63SMESG000039018.1[more]
SMESG000071716.17.928e-7646.15SMESG000071716.1[more]
SMESG000014158.11.747e-6573.85SMESG000014158.1[more]
SMESG000058084.12.695e-6442.95SMESG000058084.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034441 ID=SMED30034441|Name=SMED30034441|organism=Schmidtea mediterranea sexual|type=transcript|length=1522bp
AATATATATATATATATATTCAAACAGGTTTTGAAAAGTCGTTTTGGGGA
TAATATGATAGGAATTGTATATATTTGTATTACTATTATTCTTTTGCGAT
TATTCTTCTAAAGATAATGATGAACTTTTCTAACCAATCTTATTCAGGAA
AATCAGGACCGTTGATTTATGTCCCCACTCATGTTGCCGATCGGTGGAGG
CAAGCGTGGAGACGATTCGGACAAGAAAGATGTCCCGAGTTTTCCCGATC
AGAGTCCCGACGACTTAGCTGGCAATCGGGGGAAAGTAACCGGGAATCAT
GGTTGCCTGACCAAAAAAGGGAGAAGTGGAGTCCGGTTTGGGAGATCCGT
GAACATGCCCGCCACCTCCTCGGTCGCCTCGAAAGCCATCAACGACAGGT
GGACCTGCATGTGGTCAGAGCCCGTCAATACTTGGCGAACATCGAGGAGG
ACATCGCAACTGGCCGGATCGCCAACACCTACAGTCACCCACCACCATGC
AACTCTACGCTTAATTATACTGGCGGAAGAACCCGTAATGGTGTTCTCAA
ACTGTTCTCCGGAAGAATGGATGGAGAGAGGTTTTACGGACCTCTGATTC
CGTTGTTCCATAGTCGGGGACGTCCTAATCTGACCCATCATAATTAATAT
GGTTGAATTTTTTGCCTGAATAAATAGCTTGCCACCTTAGATGCCCATTT
TGTTTTGTTTGGTTGTTTTAGTAAAACATTTTTCCACTTATGTTTAATAG
TATTCATATTAAATAATTCTGGATTAGTAACCAACAATTTAATGTCTTTA
ATTATAGCAATGGAATCCCTACAAATATTGCGGATATAACTGGTCCGTGC
CCAGCAAACCAATAAAACTCTGTACAACCAGATCATTCAATTGACTCGGG
AGATCCATCAAACAAAAGCCACCTGGGTGGACCCGACTAAGATCAAATCA
ATACATCAAAGGCTTACCGCGGCTCAAAAGGGATGGGCAGACGAATCAAA
GCCTCCGAACACAGATACGGGGGTTGGAGGTTGCCCTGTCCGCCTGTCAG
GAAGGGGCTGCCGTAACCTACCCCTTCGTCTTTGCACCATCTTAATTGGC
CTATCGTGAGTCAGTGGCCACTCCGGCAACGGCCGCAACCCCAACCACAC
CAATAACCAATAGCTATCGGCCGGGGGTGAAAGGGGCGGGCTAGACGTAG
AGCCGCTCGATTAGCGAATAAGGCCAAATTAACTTAAAAGTGCTTTAACT
TGTGAATTATATATGTCTAATTATAAATTATATATTTCTTGTTATTCGAA
GCGATGTCCTTAAAGCTTGATAAGTATCGAAAACCCCGCAATCAATACAC
TAGTACTCACATTTCGACATGTAGCCGTTCTCTTATTTTCTAGGAACAAC
ATTATCGGATTTCGTTTTCACTATGATGAACTCCAATCATAAAACCTACT
ATACACAAGGGACTTTCAAAGCGAGCATAAGTCTTCTAACGACAGCTGGT
TGGACCCAGGGATTGTCCGAGC
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protein sequence of SMED30034441-orf-1

>SMED30034441-orf-1 ID=SMED30034441-orf-1|Name=SMED30034441-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MSPLMLPIGGGKRGDDSDKKDVPSFPDQSPDDLAGNRGKVTGNHGCLTKK
GRSGVRFGRSVNMPATSSVASKAINDRWTCMWSEPVNTWRTSRRTSQLAG
SPTPTVTHHHATLRLIILAEEPVMVFSNCSPEEWMERGFTDL*
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protein sequence of SMED30034441-orf-2

>SMED30034441-orf-2 ID=SMED30034441-orf-2|Name=SMED30034441-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=177bp
MMNFSNQSYSGKSGPLIYVPTHVADRWRQAWRRFGQERCPEFSRSESRRL
SWQSGESNRESWLPDQKREKWSPVWEIREHARHLLGRLESHQRQVDLHVV
RARQYLANIEEDIATGRIANTYSHPPPCNSTLNYTGGRTRNGVLKLFSGR
MDGERFYGPLIPLFHSRGRPNLTHHN*
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