SMED30003626

Overview
NameSMED30003626
Smed IDSMED30003626
Length (bp)874
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 SMED30003626 (SMED30003626) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003626 (SMED30003626) 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 SMED30003626 (SMED30003626) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003626 (SMED30003626) 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



SMED30003626

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30003626SMESG000075442.1 SmedASXL_077059SmedAsxl_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
SMED30003626 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000185:91907..92966 -4214
v31.010290:17700..18499 -2599
v31.001691:10750..11584 +2305
Homology
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BLAST of SMED30003626 vs. Planmine SMEST
Match: SMESG000075442.1 (SMESG000075442.1)

HSP 1 Score: 554.288 bits (1427), Expect = 0.000e+0
Identity = 281/281 (100.00%), Postives = 281/281 (100.00%), Query Frame = 1 
Query:   13 RSINFFQISTSFITLLPKSENYAFHMYSNLVNLLKYASQACNSERPLLCIEKYTSDDDGSMKLIISRFTVITWEXXXXXXXXXXXDFWTESTLNMPLKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFDKIAVLFEPNVKILTKDWIDSVFENQYLAHCSCKN 855
            RSINFFQISTSFITLLPKSENYAFHMYSNLVNLLKYASQACNSERPLLCIEKYTSDDDGSMKLIISRFTVITWELLLYYINNNLLDFWTESTLNMPLKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFDKIAVLFEPNVKILTKDWIDSVFENQYLAHCSCKN
Sbjct:    5 RSINFFQISTSFITLLPKSENYAFHMYSNLVNLLKYASQACNSERPLLCIEKYTSDDDGSMKLIISRFTVITWELLLYYINNNLLDFWTESTLNMPLKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFDKIAVLFEPNVKILTKDWIDSVFENQYLAHCSCKN 285
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BLAST of SMED30003626 vs. Planmine SMEST
Match: SMESG000075258.1 (SMESG000075258.1)

HSP 1 Score: 393.275 bits (1009), Expect = 1.094e-138
Identity = 208/280 (74.29%), Postives = 231/280 (82.50%), Query Frame = 1 
Query:   13 RSINFFQISTSFITLLPKSENYAFHMYSNLVNLLKYASQACNSERPLLCIEKYTSDDDGSMKLIISRFTVITWEXXXXXXXXXXXDFWTESTLNMPLKDYVICLDNIPSTDNLQ-FNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFDK--IAVLFEPNVKILTKDWIDSVFENQYLAHC 843
            R IN FQI T  I  LPK EN  F +YSNL NLLKYA Q C+ ERPLLCIEKYTS+DD  MK  +S FT+IT EL+++YINN+LL+FW EST+N PLKDYVICLDNIPS+D+LQ  +YVTKMKLMGAIIK DFDETVKYAIITGIEYS NIE+FVKFYKSRENVLN  WID CY+SMLMKGEGSE AKL+ CKLFHGFN+ P YR P PSE L K LLEL +NGASI  LY+ S NAVILEEDDDYF+K  IA L+EPNV+ILTK WIDSVFENQYL HC
Sbjct:    5 RIINLFQIPTIRIPHLPKLENVCFILYSNLENLLKYAPQTCHLERPLLCIEKYTSEDDNLMKFFVSDFTIITLELIIFYINNSLLEFWCESTINFPLKDYVICLDNIPSSDDLQVLDYVTKMKLMGAIIKYDFDETVKYAIITGIEYSNNIEQFVKFYKSRENVLNYTWIDTCYKSMLMKGEGSENAKLHTCKLFHGFNICPFYRLPRPSEELSKCLLELIENGASILNLYDASANAVILEEDDDYFNKLHIAALYEPNVQILTKYWIDSVFENQYLGHC 284
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BLAST of SMED30003626 vs. Planmine SMEST
Match: SMESG000041233.1 (SMESG000041233.1)

HSP 1 Score: 297.745 bits (761), Expect = 5.400e-102
Identity = 158/221 (71.49%), Postives = 185/221 (83.71%), Query Frame = 1 
Query:  193 MKLIISRFTVITWEXXXXXXXXXXXDFWTESTLNMPLKDYVICLDNIPSTDNLQF-NYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFD--KIAVLFEPNVKILTKDWIDSVFENQYLAHCS 846
            MKL ++ FT+IT E+L++YI N+LLDFW EST+++PLK YVICLDNIPS+DNL+  N VTKMKLMGAIIK++FDETVKYAIITGIEYSKNIE+FVKFYKSRENVLN  WID CYRSMLMK EGSEIAKL  CKLFHGFN+ P YR P   E+LKKRL++L DNGASIS LY+ S NAVI+E  D+Y D  +I  L+EP+VK++T DWIDSV ENQYL  CS
Sbjct:    1 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLEVSNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKFYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIE--DNYPDSFQIPFLYEPDVKLVTNDWIDSVIENQYLGPCS 219
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BLAST of SMED30003626 vs. Planmine SMEST
Match: SMESG000041233.1 (SMESG000041233.1)

HSP 1 Score: 301.212 bits (770), Expect = 1.665e-99
Identity = 158/221 (71.49%), Postives = 185/221 (83.71%), Query Frame = 1 
Query:  193 MKLIISRFTVITWEXXXXXXXXXXXDFWTESTLNMPLKDYVICLDNIPSTDNLQF-NYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFD--KIAVLFEPNVKILTKDWIDSVFENQYLAHCS 846
            MKL ++ FT+IT E+L++YI N+LLDFW EST+++PLK YVICLDNIPS+DNL+  N VTKMKLMGAIIK++FDETVKYAIITGIEYSKNIE+FVKFYKSRENVLN  WID CYRSMLMK EGSEIAKL  CKLFHGFN+ P YR P   E+LKKRL++L DNGASIS LY+ S NAVI+E  D+Y D  +I  L+EP+VK++T DWIDSV ENQYL  CS
Sbjct:    1 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLEVSNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKFYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIE--DNYPDSFQIPFLYEPDVKLVTNDWIDSVIENQYLGPCS 219
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BLAST of SMED30003626 vs. Planmine SMEST
Match: SMESG000015104.1 (SMESG000015104.1)

HSP 1 Score: 164.851 bits (416), Expect = 2.206e-50
Identity = 103/175 (58.86%), Postives = 120/175 (68.57%), Query Frame = 1 
Query:   64 KSENYAFHMYSNLVNLLKYASQA-CNSERPLLCIEKYTSDDDGSMKLIISRFTVITWEXXXXXXXXXXXDFWTESTLNMPLKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYAC 585
            K+EN+  ++   +  +L+ A+ A    E P         +DD SMKL ISRFTVIT E LLY++NNNLL+FW ESTLNMPLKDY +CLDNIP TDNL+F+YVTKMKLMGAIIK+DFDETVK  IIT IEY+KNIEK                      SMLMKGEGSEIAKLYAC
Sbjct:   38 KAENHNLNL-DEICEILQLAATAIVGVENP--------KEDDASMKLKISRFTVITLEFLLYFMNNNLLEFWNESTLNMPLKDYAMCLDNIPCTDNLRFDYVTKMKLMGAIIKEDFDETVKSGIITAIEYNKNIEK----------------------SMLMKGEGSEIAKLYAC 181
The following BLAST results are available for this feature:
BLAST of SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 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 SMED30003626 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000075442.10.000e+0100.00SMESG000075442.1[more]
SMESG000075258.11.094e-13874.29SMESG000075258.1[more]
SMESG000041233.15.400e-10271.49SMESG000041233.1[more]
SMESG000041233.11.665e-9971.49SMESG000041233.1[more]
SMESG000015104.12.206e-5058.86SMESG000015104.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003626 ID=SMED30003626|Name=SMED30003626|organism=Schmidtea mediterranea sexual|type=transcript|length=874bp
TCTTCCGATCTGAGAAGTATTAATTTTTTTCAAATATCCACCAGCTTCAT
AACTCTTTTACCTAAATCTGAAAATTATGCTTTTCATATGTATTCAAATT
TGGTAAATTTATTAAAATATGCATCACAAGCTTGCAATTCTGAACGTCCA
CTTCTCTGTATCGAAAAGTATACTTCAGATGATGATGGATCAATGAAGCT
TATAATCTCTCGTTTTACAGTTATAACTTGGGAGTTACTATTATACTATA
TAAACAATAATCTTCTTGATTTTTGGACTGAATCTACTCTTAATATGCCA
TTAAAAGATTATGTAATATGTCTTGATAATATCCCTAGTACTGATAATTT
GCAATTTAATTATGTTACAAAAATGAAACTAATGGGAGCTATTATCAAAG
ATGACTTTGATGAAACTGTTAAATATGCCATTATTACAGGAATAGAATAC
AGCAAAAATATTGAAAAGTTTGTTAAGTTTTATAAGAGTCGAGAAAATGT
CTTGAATTGTAACTGGATTGATATGTGTTATAGATCAATGTTAATGAAAG
GCGAAGGCAGTGAAATTGCAAAATTGTATGCATGCAAACTTTTTCATGGT
TTCAATGTTGTTCCTTGCTATCGACCGCCTAGTCCATCCGAAGCGCTAAA
GAAACGCTTATTGGAGCTATTTGACAATGGCGCAAGTATTTCAACTCTTT
ATGAGCAGTCGACAAATGCTGTGATTCTTGAGGAAGATGATGATTATTTC
GATAAAATCGCAGTATTGTTCGAGCCCAATGTGAAAATACTGACCAAAGA
TTGGATTGACAGTGTGTTTGAGAATCAGTATTTGGCGCACTGCAGTTGTA
AAAATTAATTGGTTTTATAATTAT
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protein sequence of SMED30003626-orf-1

>SMED30003626-orf-1 ID=SMED30003626-orf-1|Name=SMED30003626-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=286bp
SSDLRSINFFQISTSFITLLPKSENYAFHMYSNLVNLLKYASQACNSERP
LLCIEKYTSDDDGSMKLIISRFTVITWELLLYYINNNLLDFWTESTLNMP
LKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEY
SKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHG
FNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYF
DKIAVLFEPNVKILTKDWIDSVFENQYLAHCSCKN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036420BRCT_dom_sf
IPR001357BRCT_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036420BRCT domain superfamilyGENE3DG3DSA:3.40.50.10190coord: 87..180
e-value: 1.5E-6
score: 30.1
IPR036420BRCT domain superfamilySUPERFAMILYSSF52113BRCT domaincoord: 61..174
IPR036420BRCT domain superfamilySUPERFAMILYSSF52113BRCT domaincoord: 149..274
NoneNo IPR availableCDDcd17740BRCT_Rad4_rpt1coord: 94..174
e-value: 6.54357E-5
score: 38.612