SMED30010861

Overview
NameSMED30010861
Smed IDSMED30010861
Length (bp)784
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 SMED30010861 (SMED30010861) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010861 (SMED30010861) 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 SMED30010861 (SMED30010861) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010861 (SMED30010861) 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




SMED30010861

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
tailSMED30010861SMESG000063974.1 SmedASXL_013269SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
tailSMED30010861SMESG000063974.1 dd_Smed_v6_14268_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30010861SMESG000063974.1 dd_Smed_v4_14268_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30010861SMESG000063974.1 dd_Smed_v4_14268_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
SMED30010861 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000513:1610..2393 +3902
Homology
BLAST of SMED30010861 vs. TrEMBL
Match: gnl|BL_ORD_ID|17041442 (tr|A0A1S3JIW3|A0A1S3JIW3_LINUN uncharacterized protein LOC106151564 isoform X2 OS=Lingula unguis OX=7574 GN=LOC106173473 PE=4 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 5.971e-12
Identity = 55/192 (28.65%), Postives = 92/192 (47.92%), Query Frame = 3
Query:  171 LKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQK 746
            +K D  + LKK N L  Q+  W    +  F   L +VQ     L+ + + T+ +F  +L+    L      R  + E L EF + W  L  L      +V ++T EF ES   L+ P+   ++  L + +     +D+ F ++ H + + LFT+ M   +    G L+ YIPY+L    K C+L+ K+ I+K
Sbjct:   57 VKKDALAHLKKYNALRTQFIEWFSANNKAFCVALQTVQLAVPDLVPRDIYTMNDFIKVLEMCRLLLSKKRWRLTSHEKLEEFYEFWTRLSELKAMGDKNVYERTCEFCESITRLREPQIKDKIDRLYAKLNKEYSNDFIFKEI-HNERDNLFTYRMMQPA--FLG-LISYIPYLLKNATKVCYLVTKLHIEK 244          
BLAST of SMED30010861 vs. TrEMBL
Match: gnl|BL_ORD_ID|20320393 (tr|A0A1S3H4G0|A0A1S3H4G0_LINUN uncharacterized protein LOC106151564 isoform X1 OS=Lingula unguis OX=7574 GN=LOC106151564 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 1.413e-11
Identity = 54/192 (28.12%), Postives = 91/192 (47.40%), Query Frame = 3
Query:  171 LKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQK 746
            +K D  + LKK N L  Q+  W    +  F   L +VQ     L+ + + T+ +F  +L+    L      R  + E L EF + W  L  L      +V ++T EF ES   L+ P+   ++  L + +     +D+ F ++ H + + LFT+ M   +      L+ YIPY+L    K C+L+ K+ I+K
Sbjct:   94 VKKDALAHLKKYNALRTQFIEWFSANNKAFCVALQTVQLAVPDLVPRDIYTMNDFIKVLEMCRLLLSKKRWRLTSHEKLEEFYEFWTRLSELKAMGDKNVYERTCEFCESITRLREPQIKDKIDRLYAKLNKEYSNDFIFKEI-HNERDNLFTYRMMQPA---FLGLISYIPYLLKNATKVCYLVTKLHIEK 281          
BLAST of SMED30010861 vs. TrEMBL
Match: gnl|BL_ORD_ID|18209042 (tr|A0A267GS40|A0A267GS40_9PLAT Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig019887g1 PE=4 SV=1)

HSP 1 Score: 68.9366 bits (167), Expect = 3.374e-10
Identity = 58/227 (25.55%), Postives = 102/227 (44.93%), Query Frame = 3
Query:   69 SNVSLSLCDH-RVPTQPTERKWPDILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETI---TLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFD-KLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKI 734
            S V L+L D       PT R+ P    ++ ++   L+A  + + K  N   + Y+ WH +KS  F   L  +QC+ S     ++ +I EF+ L  +      LQ         L+ ++EF   W +   L E F    ++  +   E+    + P   ++LL+L   + A  +SD RFD    H   E LFT+ +    +   G L+  +P +L   ++ C+  E++
Sbjct:    2 SQVRLALSDPISSSAAPTVRE-PATNRERLDQ---LQATAQRYRKVFNARRVAYKDWHSNKSASFLEALKRLQCIASSSSAPTVASIAEFRELRAQAADLRRLQPQRGAAAAELQRVDEFLNHWRDYLALKEIFELEFVRPLARLLEATEAFRYPAMRADLLKLMERLDA--ESDERFDFSGLHNTTENLFTYRVPLRDERFLG-LMQILPRLLQTGSQVCYFTEQL 221          
BLAST of SMED30010861 vs. TrEMBL
Match: gnl|BL_ORD_ID|18328482 (tr|A0A267FJG4|A0A267FJG4_9PLAT Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig002494g1 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 2.998e-8
Identity = 59/227 (25.99%), Postives = 102/227 (44.93%), Query Frame = 3
Query:   69 SNVSLSLCDH-RVPTQPTERKWPDILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETI---TLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFD-KLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKI 734
            S V L+L D       PT R+ P    ++ ++   L+A  + + K  N   + Y+ WH +KS  F   L  +QC+ S     S+ +I EF+ L  +      LQ         L+ ++EF   W +   L E F    ++  +   E+    + P   ++LL+L   + A  +SD RFD    H   E LFT+ +    +   G L+  +P +L   ++ C+  E++
Sbjct:    2 SQVRLALSDPISSSAAPTVRE-PATNRERLDQ---LQATAQRYRKAFNARRVAYKDWHSNKSASFLEALKRLQCIASSSSAPSIASIAEFRELRAQAADLRRLQPQKGAAAAELQRIDEFLNHWRDYLALKEIFEREFVRPLARLLEATEAFRYPAMRADLLKLMERLDA--ESDERFDFSGLHNTTENLFTYRVPLRDERFLG-LMQILPRLLQTGSQVCYFTEQL 221          
BLAST of SMED30010861 vs. TrEMBL
Match: gnl|BL_ORD_ID|15740424 (tr|R7TVK4|R7TVK4_CAPTE Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_224281 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 2.184e-7
Identity = 51/213 (23.94%), Postives = 87/213 (40.85%), Query Frame = 3
Query:  135 DILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETIT---LQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNS-------VMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQ 743
            D+  ++ +  L LK      +   N L   Y  W K +   F   + SVQ +   L+ + +RT+ EF++L    +    L   G+     +     F   W     L  E  N        ++ K   F  + A+ ++ +   EL E C         D+ F ++ H +   LFT+ +  S     G LV Y+P++L    K C L+ K+ I+
Sbjct:   23 DLFRERSHALLKLKKRSNILMADFNRLYSDYSDWFKRQERSFIGAIKSVQLVIPTLVPRDIRTVTEFRHLSSMAMRIDCLAASGAQAQFKI-----FENFWIKFMELKNELENEFLPELDVLIAKVDTFRANGAQAKIEKLRRELFENCGI-------DYDFSRV-HDERNHLFTYRLMVSDQGFLG-LVGYLPFLLNFAIKICFLVNKLFIE 221          
BLAST of SMED30010861 vs. Planmine SMEST
Match: SMESG000063974.1 (SMESG000063974.1)

HSP 1 Score: 488.419 bits (1256), Expect = 1.329e-177
Identity = 236/236 (100.00%), Postives = 236/236 (100.00%), Query Frame = 3
Query:   42 MKNRDSDKYSNVSLSLCDHRVPTQPTERKWPDILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQKA 749
            MKNRDSDKYSNVSLSLCDHRVPTQPTERKWPDILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQKA
Sbjct:    1 MKNRDSDKYSNVSLSLCDHRVPTQPTERKWPDILTKKYNEELALKADVKSFLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQNLLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEFYESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMNASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQKA 236          
The following BLAST results are available for this feature:
BLAST of SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 vs. UniProt
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 SMED30010861 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
gnl|BL_ORD_ID|170414425.971e-1228.65tr|A0A1S3JIW3|A0A1S3JIW3_LINUN uncharacterized pro... [more]
gnl|BL_ORD_ID|203203931.413e-1128.13tr|A0A1S3H4G0|A0A1S3H4G0_LINUN uncharacterized pro... [more]
gnl|BL_ORD_ID|182090423.374e-1025.55tr|A0A267GS40|A0A267GS40_9PLAT Uncharacterized pro... [more]
gnl|BL_ORD_ID|183284822.998e-825.99tr|A0A267FJG4|A0A267FJG4_9PLAT Uncharacterized pro... [more]
gnl|BL_ORD_ID|157404242.184e-723.94tr|R7TVK4|R7TVK4_CAPTE Uncharacterized protein OS=... [more]
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BLAST of SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 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 SMED30010861 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000063974.11.329e-177100.00SMESG000063974.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010861 ID=SMED30010861|Name=SMED30010861|organism=Schmidtea mediterranea sexual|type=transcript|length=784bp
CGAAAAGGTAACCAACAGAAAGAATGCAGTAGTATTTATAAATGAAAAAT
AGAGACAGTGATAAATACAGCAATGTTTCGTTATCTTTATGCGATCATCG
AGTTCCCACGCAACCAACAGAACGAAAATGGCCAGATATCTTAACCAAAA
AATACAATGAAGAATTAGCATTGAAAGCCGACGTAAAGAGTTTTCTTAAA
AAGGTAAATGGTTTATTAATTCAATATCAAACTTGGCATAAACATAAATC
GAACCGATTTTTTACAGTTCTTCATTCGGTTCAATGTCTTACGAGTGGAT
TAATCATCAAATCTCTTCGTACTATTGGGGAGTTTCAGAATCTTCTGAAA
GAAACAATAACTTTGCAGAAACATGGCAGTATTCGACACATTAATTTGGA
GATTCTTAATGAATTTTCTCAAATGTGGAATAATCTTCAGTTATTGGTGG
AAGAATTCCGAAACTCAGTGATGCAGAAAACTTCGGAATTTTACGAATCG
GCGGCCGAGTTACAAGTCCCTGAGTATTATTCTGAATTACTCGAATTGTG
TAGCTACATTTTCGCTATCTGCAAATCCGACTGGAGGTTCGATAAATTGA
AGCATTTGGACAACGAATGTCTTTTCACTTTTTCAATGAATGCTTCATCA
GATGACTTAGAAGGAAATTTGGTCTATTATATTCCATATATCCTTGGGAT
AATCGCAAAGACTTGTCACTTAATTGAAAAAATACGAATTCAAAAAGCAT
GAAAATTTGTTTTAATTTTACCAATTGAATCTGA
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protein sequence of SMED30010861-orf-1

>SMED30010861-orf-1 ID=SMED30010861-orf-1|Name=SMED30010861-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=237bp
MKNRDSDKYSNVSLSLCDHRVPTQPTERKWPDILTKKYNEELALKADVKS
FLKKVNGLLIQYQTWHKHKSNRFFTVLHSVQCLTSGLIIKSLRTIGEFQN
LLKETITLQKHGSIRHINLEILNEFSQMWNNLQLLVEEFRNSVMQKTSEF
YESAAELQVPEYYSELLELCSYIFAICKSDWRFDKLKHLDNECLFTFSMN
ASSDDLEGNLVYYIPYILGIIAKTCHLIEKIRIQKA*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000096ventral epidermis
PLANA:0000421tail