SMED30020520

Overview
NameSMED30020520
Smed IDSMED30020520
Length (bp)651
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 SMED30020520 (SMED30020520) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020520 (SMED30020520) 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 SMED30020520 (SMED30020520) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020520 (SMED30020520) 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




SMED30020520

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
neoblastSMED30020520 dd_Smed_v4_20291_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
Homology
BLAST of SMED30020520 vs. TrEMBL
Match: T1F5G4 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20204063 PE=4 SV=1)

HSP 1 Score: 184.496 bits (467), Expect = 6.300e-51
Identity = 86/130 (66.15%), Postives = 107/130 (82.31%), Query Frame = -2
Query:    3 ILLIGHPKNMITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 392
            I LIG PK  I+GARLPSG+D+M+NFV+Y R QKL + ++AQQV +QLLPFW+KSR+PVR KPHIIQKIKDL+   V L+ HR RNNS DQ+NQK+Y +KL +LFDISHAN  +LIKN++DR F KLQQ+
Sbjct:   13 IWLIGFPKETISGARLPSGQDVMKNFVFYHRVQKLNINKAAQQVHEQLLPFWVKSRLPVRQKPHIIQKIKDLYADQVRLMKHRKRNNSTDQMNQKQYINKLSQLFDISHANSEQLIKNDKDRQFLKLQQQ 142          
BLAST of SMED30020520 vs. TrEMBL
Match: A0A4Y2RRB7 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_40026_1 PE=4 SV=1)

HSP 1 Score: 121.324 bits (303), Expect = 7.124e-31
Identity = 65/119 (54.62%), Postives = 88/119 (73.95%), Query Frame = -2
Query:    6 ITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQ 362
            I GA LPS +D+ RNF+Y++R QK T++ SA  V +Q++PFW KSR+ VR K H++++IKDL+ +   L+  R RNN+KDQ NQK Y + L KLFDISHAN  EL+KN EDR F +LQ+
Sbjct:    4 IKGACLPSRQDVTRNFIYFRRFQKHTISRSAVLVYNQIVPFWEKSRLLVRDKQHVLKQIKDLYGKQENLMKQRKRNNAKDQENQKIYCNNL-KLFDISHANSQELLKN-EDRKFLQLQR 120          
BLAST of SMED30020520 vs. TrEMBL
Match: A0A2S2PRS5 (Uncharacterized protein OS=Schizaphis graminum OX=13262 GN=g.113932 PE=4 SV=1)

HSP 1 Score: 94.3597 bits (233), Expect = 1.717e-20
Identity = 50/129 (38.76%), Postives = 75/129 (58.14%), Query Frame = -2
Query:    6 ILLIGHPKNMITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQ 392
            + L+G  KN ITG +LPS RDI+    Y  R   L++ ESA  V D+ L +W K+RIP  H+   I K K L+     L  H++R +  ++  +K++ D L  LFDI+HA+   +IK +ED+ F   Q+
Sbjct:    6 VFLVGIMKNQITGGKLPSKRDILSVLFYNMRVVNLSLQESASLVIDECLIYWKKARIPTHHRSDCIAKCKKLYTDLRILEKHKARTSELNKNKRKKFEDGLKDLFDIAHADALSMIKIDEDKQFLIAQR 134          
BLAST of SMED30020520 vs. TrEMBL
Match: A0A4Y2ID55 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_195305_1 PE=4 SV=1)

HSP 1 Score: 93.5893 bits (231), Expect = 8.629e-20
Identity = 51/130 (39.23%), Postives = 73/130 (56.15%), Query Frame = -2
Query:    3 ILLIGHPKNMITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 392
            I LIG  ++ ITG +LPS R ++    Y     KL++ ESA  V  + L FW K+RIP R  PH ++KI  ++     L     R +   + N++ +   L+ LFDI+HAN  E+IK EEDR F   Q+E
Sbjct:   12 IYLIGSERHQITGCKLPSNRQVLSVLFYNLHEVKLSIRESANLVVRECLIFWEKARIPTRATPHCVEKIMKMYNYWSNLQKSACRRSETQEENERNFISDLNNLFDIAHANALEIIKIEEDRKFLLSQRE 141          
BLAST of SMED30020520 vs. TrEMBL
Match: A0A4Y2BG11 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_195068_1 PE=4 SV=1)

HSP 1 Score: 96.6709 bits (239), Expect = 8.735e-20
Identity = 51/130 (39.23%), Postives = 73/130 (56.15%), Query Frame = -2
Query:    3 ILLIGHPKNMITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 392
            I LIG  ++ ITG +LPS R ++    Y     KL++ ESA  V  + L FW K+RIP R  PH ++KI  ++     L     R +   + N++ +   L+ LFDI+HAN  E+IK EEDR F   Q+E
Sbjct:   12 IYLIGSERHQITGCKLPSNRQVLSMLFYNLHEVKLSIRESANSVVRECLIFWEKARIPTRATPHCVEKIMKMYNYWCSLQKSACRRSETQEENERNFISDLNNLFDIAHANAMEIIKIEEDRKFLLSQRE 141          
BLAST of SMED30020520 vs. Planmine SMEST
Match: SMESG000078047.1 (SMESG000078047.1)

HSP 1 Score: 184.882 bits (468), Expect = 5.285e-60
Identity = 89/99 (89.90%), Postives = 93/99 (93.94%), Query Frame = -2
Query:   69 MITGARLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDIS 365
            MIT ARLPSGRDIMRNFVYY+RNQKL VAESAQ+V DQLL FW KSRIPVRHKP IIQKIK+L+CQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDIS
Sbjct:    1 MITSARLPSGRDIMRNFVYYRRNQKLAVAESAQRVYDQLLQFWTKSRIPVRHKPQIIQKIKNLYCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDIS 99          
BLAST of SMED30020520 vs. Planmine SMEST
Match: SMESG000064988.1 (SMESG000064988.1)

HSP 1 Score: 187.578 bits (475), Expect = 1.140e-55
Identity = 91/103 (88.35%), Postives = 95/103 (92.23%), Query Frame = -2
Query:    3 YYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 311
            +Y RNQKLT+AES Q+V DQLLPFW KSRI VRHKPHIIQKIKDLHCQ+VGLV HRSRNNSKDQLNQKEYNDKLDKLFDISHANC ELIKNEEDRMF KLQQE
Sbjct:  150 HYHRNQKLTIAESTQRVYDQLLPFWTKSRIQVRHKPHIIQKIKDLHCQYVGLVKHRSRNNSKDQLNQKEYNDKLDKLFDISHANCYELIKNEEDRMFLKLQQE 252          
BLAST of SMED30020520 vs. Planmine SMEST
Match: SMESG000038763.1 (SMESG000038763.1)

HSP 1 Score: 152.14 bits (383), Expect = 1.248e-43
Identity = 73/77 (94.81%), Postives = 75/77 (97.40%), Query Frame = -2
Query:    3 KSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 233
            KSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDK++KLFDISHANCNELIKNEED MF KLQQE
Sbjct:   18 KSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLNQKEYNDKIEKLFDISHANCNELIKNEEDSMFLKLQQE 94          
BLAST of SMED30020520 vs. Planmine SMEST
Match: SMESG000028097.1 (SMESG000028097.1)

HSP 1 Score: 98.2117 bits (243), Expect = 2.167e-24
Identity = 47/51 (92.16%), Postives = 49/51 (96.08%), Query Frame = -2
Query:    3 VNHRSRNNSKDQLNQKEYNDKLDKLFDISHANCNELIKNEEDRMFWKLQQE 155
            + HRSRNNSKDQLNQKEYNDKLDK+FDISHANCNELIKNEEDRMF KLQQE
Sbjct:    1 MKHRSRNNSKDQLNQKEYNDKLDKMFDISHANCNELIKNEEDRMFLKLQQE 51          
BLAST of SMED30020520 vs. Planmine SMEST
Match: SMESG000000162.1 (SMESG000000162.1)

HSP 1 Score: 70.8626 bits (172), Expect = 3.141e-14
Identity = 39/128 (30.47%), Postives = 63/128 (49.22%), Query Frame = -2
Query:   21 ILLIGHPKNMITGA---RLPSGRDIMRNFVYYQRNQKLTVAESAQQV*DQLLPFWIKSRIPVRHKPHIIQKIKDLHCQHVGLVNHRSRNNSKDQLN-QKEYNDKLDKLFDISHANCNELIKNEEDRMF 392
            I L+G P   I      +LP+    +R      +  K T+A +   + D++L +W K+ IP   KPH++ K+K LH  H  +  H+ R +S  Q+  + ++  K+  L DI+HA         EDR F
Sbjct:   25 IWLVGQPLTSIDEVEPRQLPTNGLALRRIYCEMKTNKATLAATFSTLADEVLSYWAKANIPTTAKPHVVAKLKSLHQDHATVSKHKQRQHSASQIGLETDFTLKMGHLLDIAHAEWEHKTFIPEDRQF 152          
The following BLAST results are available for this feature:
BLAST of SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
T1F5G46.300e-5166.15Uncharacterized protein OS=Helobdella robusta OX=6... [more]
A0A4Y2RRB77.124e-3154.62Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A2S2PRS51.717e-2038.76Uncharacterized protein OS=Schizaphis graminum OX=... [more]
A0A4Y2ID558.629e-2039.23Uncharacterized protein OS=Araneus ventricosus OX=... [more]
A0A4Y2BG118.735e-2039.23Uncharacterized protein OS=Araneus ventricosus OX=... [more]
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BLAST of SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 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 SMED30020520 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000078047.15.285e-6089.90SMESG000078047.1[more]
SMESG000064988.11.140e-5588.35SMESG000064988.1[more]
SMESG000038763.11.248e-4394.81SMESG000038763.1[more]
SMESG000028097.12.167e-2492.16SMESG000028097.1[more]
SMESG000000162.13.141e-1430.47SMESG000000162.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020520 ID=SMED30020520|Name=SMED30020520|organism=Schmidtea mediterranea sexual|type=transcript|length=651bp
TACTCTTGCTGCAACTTCCAAAACATGCGGTCTTCCTCGTTCTTTATCAG
TTCATTACAGTTAGCATGACTGATATCGAACAGCTTGTCTAATTTATCAT
TGTATTCTTTCTGATTCAGCTGATCCTTAGAGTTATTTCTTGAACGATGG
TTCACCAATCCAACATGCTGACAATGGAGATCTTTAATCTTCTGAATGAT
GTGTGGTTTGTGGCGAACTGGAATTCGAGACTTTATCCAGAACGGCAAGA
GTTGATCTTACACTTGCTGTGCACTTTCAGCAACTGTCAATTTCTGATTT
CGTTGATAGTAAACAAAGTTCCTCATTATGTCACGACCAGAAGGAAGGCG
AGCACCTGTTATCATATTTTTGGGGTGTCCAATCAACAAGATTATATCCC
TACTACGAGTACCAGTCGTCGCGGTCGAGGTCGAGGCGGCCATTATGTCG
GATTTTCTGTAAATAATAATAATAAACAAGCTGTACCGCATTAATATGAT
GTATTATACATAATCAATACGCAGTCACCAGACTAAACAATGCACTGAAT
CAGTCGTAAATGGAATAGATAGCACTAAAATAAGGTAATGAACCAATCGG
TTATGTATTCAAAAGTAGGTTCAAAAGTAGCCTTGATAGGTGTTGAAGCA
C
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