SMED30018612

Overview
NameSMED30018612
Smed IDSMED30018612
Length (bp)903
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 SMED30018612 (SMED30018612) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018612 (SMED30018612) 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 SMED30018612 (SMED30018612) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018612 (SMED30018612) 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




SMED30018612

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30018612h1SMcG0011461 SmedASXL_013706SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30018612h1SMcG0011461 SmedASXL_013707SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30018612h1SMcG0011461 dd_Smed_v4_8247_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30018612h1SMcG0011461 dd_Smed_v4_8247_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30018612h1SMcG0011461 dd_Smed_v4_8247_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
SMED30018612 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000061:42066..43164 -4327
v31.000081:161024..162122 -3038
Homology
BLAST of SMED30018612 vs. Planmine SMEST
Match: SMESG000041233.1 (SMESG000041233.1)

HSP 1 Score: 447.973 bits (1151), Expect = 3.641e-161
Identity = 221/224 (98.66%), Postives = 222/224 (99.11%), Query Frame = 2
Query:  191 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLE-SNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYESDVKLVTNDWIDSVIENQYLGPCSSVMSL 859
            MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLE SNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVK+YKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYE DVKLVTNDWIDSVIENQYLGPCSSVMSL
Sbjct:    1 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLEVSNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKFYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYEPDVKLVTNDWIDSVIENQYLGPCSSVMSL 224          
BLAST of SMED30018612 vs. Planmine SMEST
Match: SMESG000041233.1 (SMESG000041233.1)

HSP 1 Score: 446.047 bits (1146), Expect = 3.985e-156
Identity = 217/220 (98.64%), Postives = 218/220 (99.09%), Query Frame = 2
Query:  191 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLE-SNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYESDVKLVTNDWIDSVIENQYLGPCSS 847
            MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLE SNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVK+YKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYE DVKLVTNDWIDSVIENQYLGPCSS
Sbjct:    1 MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLEVSNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKFYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYEPDVKLVTNDWIDSVIENQYLGPCSS 220          
BLAST of SMED30018612 vs. Planmine SMEST
Match: SMESG000075258.1 (SMESG000075258.1)

HSP 1 Score: 373.244 bits (957), Expect = 1.193e-130
Identity = 188/260 (72.31%), Postives = 218/260 (83.85%), Query Frame = 2
Query:   80 YLKYSNLVNLLKYAPQSCNPDRPLLCIPRYTSDDDDLMKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLESND-VTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIE--DNYPDSFQIPFLYESDVKLVTNDWIDSVIENQYLGPCSSV 850
            ++ YSNL NLLKYAPQ+C+ +RPLLCI +YTS+DD+LMK FV+DFTIITLE++IFYI NSLL+FWCESTI+ PLK YVICLDNIPSSD+L+  D VTKMKLMGAIIK +FDETVKYAIITGIEYS NIEQFVK+YKSRENVLN  WIDTCY+SMLMK EGSE AKL+TCKLFHGFNICPFYR P   E L K L++LI+NGASI  LYD SANAVI+E  D+Y +   I  LYE +V+++T  WIDSV ENQYLG C  +
Sbjct:   28 FILYSNLENLLKYAPQTCHLERPLLCIEKYTSEDDNLMKFFVSDFTIITLELIIFYINNSLLEFWCESTINFPLKDYVICLDNIPSSDDLQVLDYVTKMKLMGAIIKYDFDETVKYAIITGIEYSNNIEQFVKFYKSRENVLNYTWIDTCYKSMLMKGEGSENAKLHTCKLFHGFNICPFYRLPRPSEELSKCLLELIENGASILNLYDASANAVILEEDDDYFNKLHIAALYEPNVQILTKYWIDSVFENQYLGHCDFI 287          
BLAST of SMED30018612 vs. Planmine SMEST
Match: SMESG000075442.1 (SMESG000075442.1)

HSP 1 Score: 366.696 bits (940), Expect = 4.337e-128
Identity = 182/254 (71.65%), Postives = 213/254 (83.86%), Query Frame = 2
Query:   89 YSNLVNLLKYAPQSCNPDRPLLCIPRYTSDDDDLMKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLESNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPESLKKRLVKLIDNGASISQLYDHSANAVIIE--DNYPDSFQIPFLYESDVKLVTNDWIDSVIENQYLGPCS 844
            YSNLVNLLKYA Q+CN +RPLLCI +YTSDDD  MKL ++ FT+IT E+L++YI N+LLDFW EST+++PLK YVICLDNIPS+DNL+ N VTKMKLMGAIIK++FDETVKYAIITGIEYSKNIE+FVK+YKSRENVLN  WID CYRSMLMK EGSEIAKL  CKLFHGFN+ P YR P   E+LKKRL++L DNGASIS LY+ S NAVI+E  D+Y D  +I  L+E +VK++T DWIDSV ENQYL  CS
Sbjct:   31 YSNLVNLLKYASQACNSERPLLCIEKYTSDDDGSMKLIISRFTVITWELLLYYINNNLLDFWTESTLNMPLKDYVICLDNIPSTDNLQFNYVTKMKLMGAIIKDDFDETVKYAIITGIEYSKNIEKFVKFYKSRENVLNCNWIDMCYRSMLMKGEGSEIAKLYACKLFHGFNVVPCYRPPSPSEALKKRLLELFDNGASISTLYEQSTNAVILEEDDDYFD--KIAVLFEPNVKILTKDWIDSVFENQYLAHCS 282          
BLAST of SMED30018612 vs. Planmine SMEST
Match: SMESG000015104.1 (SMESG000015104.1)

HSP 1 Score: 144.436 bits (363), Expect = 2.619e-42
Identity = 76/136 (55.88%), Postives = 95/136 (69.85%), Query Frame = 2
Query:  176 DDDDLMKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSSDNLESNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSRENVLNGIWIDTCYRSMLMKSEGSEIAKLNTC 583
            +DD  MKL ++ FT+ITLE L++++ N+LL+FW EST+++PLK Y +CLDNIP +DNL  + VTKMKLMGAIIKE+FDETVK  IIT IEY+KNIE                      +SMLMK EGSEIAKL  C
Sbjct:   68 EDDASMKLKISRFTVITLEFLLYFMNNNLLEFWNESTLNMPLKDYAMCLDNIPCTDNLRFDYVTKMKLMGAIIKEDFDETVKSGIITAIEYNKNIE----------------------KSMLMKGEGSEIAKLYAC 181          
The following BLAST results are available for this feature:
BLAST of SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 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 SMED30018612 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000041233.13.641e-16198.66SMESG000041233.1[more]
SMESG000041233.13.985e-15698.64SMESG000041233.1[more]
SMESG000075258.11.193e-13072.31SMESG000075258.1[more]
SMESG000075442.14.337e-12871.65SMESG000075442.1[more]
SMESG000015104.12.619e-4255.88SMESG000015104.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018612 ID=SMED30018612|Name=SMED30018612|organism=Schmidtea mediterranea sexual|type=transcript|length=903bp
GTTAATTTTTATTTATTTCAAATGGGATCTCAGAGAATTATTAACTTTTT
TCAAATATCTTCTGAGTGCATAGCTAGATTACCTAAAGTATTCAAATTTG
GTAAATTTATTAAAATATGCACCTCAGTCTTGCAATCCAGACCGTCCATT
GTTATGCATTCCAAGATATACTTCAGACGACGATGATTTAATGAAGCTTT
TTGTCGCTGATTTCACAATTATAACTTTGGAGATACTAATATTCTATATC
GAAAATAGTCTTCTTGACTTTTGGTGTGAATCGACTATTCATTTACCACT
GAAAGGTTATGTAATATGTCTTGATAATATCCCTAGTAGTGATAATTTGG
AATCTAATGATGTTACTAAAATGAAATTAATGGGAGCTATTATCAAAGAG
GAATTTGACGAAACGGTTAAATATGCTATTATTACAGGAATAGAATACAG
CAAAAATATTGAACAATTTGTTAAGTATTATAAAAGTCGAGAAAATGTAC
TGAATGGGATCTGGATTGATACCTGCTATAGATCAATGTTAATGAAAAGT
GAAGGCAGTGAAATTGCAAAATTAAATACTTGCAAACTTTTTCATGGTTT
CAATATTTGTCCTTTCTATCGACGACCTGGTCTACCCGAATCGCTAAAGA
AACGCTTAGTGAAACTAATTGACAATGGTGCAAGCATTTCACAACTTTAC
GATCATTCAGCAAATGCTGTGATTATTGAAGATAATTATCCTGATTCATT
TCAAATCCCATTTTTGTACGAGTCCGATGTGAAATTAGTGACCAACGATT
GGATTGACAGCGTAATTGAGAATCAATATTTAGGGCCCTGCAGTTCTGTA
ATGTCATTGTGATTTGTTATTATTAATAAAAAAAATTTACTTTTTTGAAA
AAA
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protein sequence of SMED30018612-orf-1

>SMED30018612-orf-1 ID=SMED30018612-orf-1|Name=SMED30018612-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=224bp
MKLFVADFTIITLEILIFYIENSLLDFWCESTIHLPLKGYVICLDNIPSS
DNLESNDVTKMKLMGAIIKEEFDETVKYAIITGIEYSKNIEQFVKYYKSR
ENVLNGIWIDTCYRSMLMKSEGSEIAKLNTCKLFHGFNICPFYRRPGLPE
SLKKRLVKLIDNGASISQLYDHSANAVIIEDNYPDSFQIPFLYESDVKLV
TNDWIDSVIENQYLGPCSSVMSL*
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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: 122..219
e-value: 4.3E-5
score: 25.6
IPR036420BRCT domain superfamilySUPERFAMILYSSF52113BRCT domaincoord: 92..216
NoneNo IPR availableCDDcd17740BRCT_Rad4_rpt1coord: 36..115
e-value: 9.085E-4
score: 35.1452