SMED30007558

Overview
NameSMED30007558
Smed IDSMED30007558
Length (bp)956
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 SMED30007558 (SMED30007558) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007558 (SMED30007558) 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 SMED30007558 (SMED30007558) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007558 (SMED30007558) 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




SMED30007558

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 cellSMED30007558SMESG000071865.1 SmedASXL_007071SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30007558SMESG000071865.1 SmedASXL_007071SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007558SMESG000071865.1 dd_Smed_v4_4209_0_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
Alignments
SMED30007558 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.003419:33172..34125 +4752
Homology
BLAST of SMED30007558 vs. TrEMBL
Match: I1ZID3 (Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.046e-8
Identity = 57/197 (28.93%), Postives = 90/197 (45.69%), Query Frame = 2
Query:  311 DTTLGIYQCKICPKHNDDYRICKFRFTKY------GSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYK----DSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF-------SMADSRRTKRGRKGKHSK 850
            +T  G + C I  +HN+   IC   F K+       SI    ILVH++ H      +   + + + L     + +K  + I+  D  L +   H  +   A +KF  C L  + DF++Y+    DS     G ++C +C +T  N ++ KF FT   S+ FTNI  HL  HF       + A SR+    +  KHS+
Sbjct:  169 ETKNGFFACSI-NQHNE---ICG-EFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSE 360          
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000071865.1 (SMESG000071865.1)

HSP 1 Score: 503.056 bits (1294), Expect = 0.000e+0
Identity = 244/244 (100.00%), Postives = 244/244 (100.00%), Query Frame = 2
Query:  122 MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV 853
            MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV
Sbjct:    1 MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV 244          
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000071713.1 (SMESG000071713.1)

HSP 1 Score: 188.734 bits (478), Expect = 5.506e-57
Identity = 104/233 (44.64%), Postives = 142/233 (60.94%), Query Frame = 2
Query:  143 IDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGK 841
            ID S + S+      N    LA+ SIH++++K A+LKF DC+LK +E FN+F  + +   G +QCKICPK +D ++  KF F+ YGS+ FMNI VHL  HFS  ES PL+RGRR +             V+  T L LCD+ Y + V D+A   F SC+LK + DF++YKD+ + L+GY++CK+C   +Q     KF FT Y SLNF+NI+ HL SHF         RGRK K
Sbjct:  146 IDVSNDISMELSFSNNDDSYLANDSIHEYVMKTASLKFKDCNLKKHEHFNIFKLNSNKLTGYFQCKICPKVHDKFKTYKFSFSNYGSLNFMNIKVHLLTHFSTKESEPLKRGRRSS-------------VLNQTQLELCDDSYSKNVIDLAANCFASCQLKTD-DFAIYKDTSNVLVGYFICKICPNDSQ--KHLKFSFTNYQSLNFSNIKTHLTSHFKKKKPIENTRGRKRK 362          
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000044230.1 (SMESG000044230.1)

HSP 1 Score: 67.0106 bits (162), Expect = 2.910e-12
Identity = 57/197 (28.93%), Postives = 90/197 (45.69%), Query Frame = 2
Query:  311 DTTLGIYQCKICPKHNDDYRICKFRFTKY------GSIQFMNILVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKYHQYVSDMALEKFDSCRLKMNKDFSLYK----DSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF-------SMADSRRTKRGRKGKHSK 850
            +T  G + C I  +HN+   IC   F K+       SI    ILVH++ H      +   + + + L     + +K  + I+  D  L +   H  +   A +KF  C L  + DF++Y+    DS     G ++C +C +T  N ++ KF FT   S+ FTNI  HL  HF       + A SR+    +  KHS+
Sbjct:  169 ETKNGFFACSI-NQHNE---ICG-EFIKFYIDQDSLSIDIEPILVHIELHLDRKSESSSIKTKSRILSSVEIDLNKSSRSIDLADAKLSNNFIHNEIIKFAEQKFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSE 360          

HSP 2 Score: 56.6102 bits (135), Expect = 7.180e-9
Identity = 49/154 (31.82%), Postives = 68/154 (44.16%), Query Frame = 2
Query:   74 NES*KIIDLTNESFSKMCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHLKVNEDFNVFT----NSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF-SLAESAPLRRGRRKTLFKTTKNTSK 520
            N+S + IDL +   S   ++ E I F+E                               KFIDCHL  + DFNV+     +S  T  G + C IC K   +    KF FT   S+ F NI+ HL+ HF S+A  A     R++T  KT K++ K
Sbjct:  238 NKSSRSIDLADAKLSNNFIHNEIIKFAEQ------------------------------KFIDCHLVQDIDFNVYEIIDDDSSLTNRGCFLCYICLKTKSNESKIKFFFTSTRSVVFTNIVAHLRIHFQSVAPFATAAVSRKRTSTKTPKHSEK 361          
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 56.6102 bits (135), Expect = 6.586e-9
Identity = 33/81 (40.74%), Postives = 47/81 (58.02%), Query Frame = 2
Query:  563 EKYHQYVSDMALEKFDSCRLKMNKDFSLY---KDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF 796
            EKY+  +   A + F  C L  + DF L     DS D L+GYY C LC +  +   + KFRF+KY+S+ +TNI  HL +H+
Sbjct:  172 EKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTD-LIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 251          

HSP 2 Score: 54.6842 bits (130), Expect = 2.256e-8
Identity = 30/74 (40.54%), Postives = 41/74 (55.41%), Query Frame = 2
Query:  230 IVKRAALKFIDCHLKVNEDFNVFTNSFDTT--LGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF 445
            IVK AA  FI+C L  + DF++     D+T  +G Y C +C          KFRF+KY S+ + NI  HLK H+
Sbjct:  178 IVKNAAKNFIECSLIPDVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 251          
BLAST of SMED30007558 vs. Planmine SMEST
Match: SMESG000047524.1 (SMESG000047524.1)

HSP 1 Score: 56.6102 bits (135), Expect = 7.078e-9
Identity = 33/81 (40.74%), Postives = 47/81 (58.02%), Query Frame = 2
Query:  563 EKYHQYVSDMALEKFDSCRLKMNKDFSLY---KDSEDPLLGYYVCKLCAETAQNRNQCKFRFTKYHSLNFTNIQFHLLSHF 796
            EKY+  +   A + F  C L  + DF L     DS D L+GYY C LC +  +   + KFRF+KY+S+ +TNI  HL +H+
Sbjct:  184 EKYYNDIVKNAAKNFIECSLIPDVDFHLSIPENDSTD-LIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 263          

HSP 2 Score: 54.6842 bits (130), Expect = 2.459e-8
Identity = 30/74 (40.54%), Postives = 41/74 (55.41%), Query Frame = 2
Query:  230 IVKRAALKFIDCHLKVNEDFNVFTNSFDTT--LGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNILVHLKKHF 445
            IVK AA  FI+C L  + DF++     D+T  +G Y C +C          KFRF+KY S+ + NI  HLK H+
Sbjct:  190 IVKNAAKNFIECSLIPDVDFHLSIPENDSTDLIGYYHCHLCTDRKKAMTKIKFRFSKYNSVIYTNINSHLKTHY 263          
The following BLAST results are available for this feature:
BLAST of SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
I1ZID31.046e-828.93Uncharacterized protein OS=Schmidtea mediterranea ... [more]
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BLAST of SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 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 SMED30007558 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071865.10.000e+0100.00SMESG000071865.1[more]
SMESG000071713.15.506e-5744.64SMESG000071713.1[more]
SMESG000044230.12.910e-1228.93SMESG000044230.1[more]
SMESG000047524.16.586e-940.74SMESG000047524.1[more]
SMESG000047524.17.078e-940.74SMESG000047524.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007558 ID=SMED30007558|Name=SMED30007558|organism=Schmidtea mediterranea sexual|type=transcript|length=956bp
TGACTCACCAAATGTAAAATCTAAAAATAAATACAAATAATTAAAAATGA
ACCAATCAGACGACTGCATAAATAACGAATCATAAAAGATTATAGATTTA
ACAAACGAATCTTTCTCAAAAATGTGTGTGAATGAAGAATGTATTGATTT
TTCAGAAAATGATAGTGTTAATAACAAAACTGATGAAAATTCGAAAATAT
CTTTGGCAAGTGGATCAATTCACAAATTTATCGTTAAACGAGCGGCTCTT
AAATTTATCGACTGCCACCTGAAGGTAAATGAAGATTTCAATGTTTTCAC
AAACAGTTTTGATACCACTTTGGGAATTTATCAATGTAAAATATGCCCGA
AACACAACGATGATTACAGAATTTGTAAATTTAGGTTTACAAAATACGGA
TCAATTCAATTTATGAATATTTTGGTTCATTTGAAAAAACACTTTAGTTT
AGCTGAAAGTGCACCTTTGAGACGAGGACGACGAAAGACTCTATTTAAAA
CAACTAAAAATACTTCGAAGCCGGAAAAAGTTATTGAATTCACGGACTTG
AATTTGTGTGATGAAAAATATCATCAATACGTATCAGACATGGCGTTGGA
AAAATTCGATTCATGTCGACTAAAAATGAATAAAGATTTCAGTCTATATA
AAGATAGTGAAGATCCACTATTGGGGTATTATGTTTGTAAATTATGTGCA
GAAACTGCTCAAAACAGAAATCAATGCAAGTTTCGTTTCACGAAGTATCA
TTCCCTCAATTTTACTAATATTCAATTTCATTTGCTCAGTCACTTTAGTA
TGGCTGATAGTCGCCGAACAAAACGCGGAAGAAAAGGAAAGCACTCTAAA
GTTTAAATATTTAATTTGTGTAAAGTAATAAATAAAATTAACTGTATGTT
CTAGTATTAACGTTTATATTTATGTAATTTTAATAATAAACTTTTAGTAA
TTGAAA
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protein sequence of SMED30007558-orf-1

>SMED30007558-orf-1 ID=SMED30007558-orf-1|Name=SMED30007558-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=245bp
MCVNEECIDFSENDSVNNKTDENSKISLASGSIHKFIVKRAALKFIDCHL
KVNEDFNVFTNSFDTTLGIYQCKICPKHNDDYRICKFRFTKYGSIQFMNI
LVHLKKHFSLAESAPLRRGRRKTLFKTTKNTSKPEKVIEFTDLNLCDEKY
HQYVSDMALEKFDSCRLKMNKDFSLYKDSEDPLLGYYVCKLCAETAQNRN
QCKFRFTKYHSLNFTNIQFHLLSHFSMADSRRTKRGRKGKHSKV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0002109X1 cell
PLANA:0002111X2 cell