SMED30003773

Overview
NameSMED30003773
Smed IDSMED30003773
Length (bp)1076
Neoblast Clusters

Zeng et. al., 2018




 



 

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




Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
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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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Alignments
SMED30003773 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001024:111066..112140 -5226
Homology
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000021279.1 (SMESG000021279.1)

HSP 1 Score: 70.0922 bits (170), Expect = 2.208e-14
Identity = 54/140 (38.57%), Postives = 79/140 (56.43%), Query Frame = -1
Query:  402 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFL-ILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILRQSQ*KG-IA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKVN 797
            ER+   M IL+EY  KF  A+LSA A  KY + S        S +L  L+++FKK +NF+ + QE  KY+Q NDS N       K+ + IL+    K  +     F A +  +  K  ++ +FKT+E++ ER+KKHEKVN
Sbjct:    7 ERVFDFMGILEEYRGKFDKAFLSANAINKYEATSEN------SNYLDCLKEAFKKPLNFMDDFQEALKYYQRNDSANEFCTKIEKLAKVILQHKLNKEKLQKFLIFHAVEDNEMNKDLRMNEFKTVEELKERLKKHEKVN 140          
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000066474.1 (SMESG000066474.1)

HSP 1 Score: 65.4698 bits (158), Expect = 6.693e-13
Identity = 37/78 (47.44%), Postives = 46/78 (58.97%), Query Frame = -1
Query:  567 FERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVNR 800
            FER   LM I KEY  KFV A+LS  ATKKY ++   +          L+++FKK MNF+ +LQE  KY Q NDS N 
Sbjct:   40 FERFFDLMWISKEYRGKFVKAFLSVNATKKYEASREDINYLDR-----LKETFKKPMNFMGDLQEAVKYRQGNDSANE 112          
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000023258.1 (SMESG000023258.1)

HSP 1 Score: 47.3654 bits (111), Expect = 4.595e-8
Identity = 44/141 (31.21%), Postives = 71/141 (50.35%), Query Frame = -1
Query:  405 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILR----QSQ*KGIA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKV 797
            ER  ++  I+ EY  KFV A+LS  +TKKY   + TL          LR +F K  + + +L E   Y Q N++         K+ + IL+    + + K    +FN L  K +K  K  K+   K+ ++M ER+K+H++V
Sbjct: 1077 ERFFEMTNIVDEYRSKFVKAFLSINSTKKYELTNETLHYTER-----LRNAFSKNRSLIDDLNEALNYRQGNEAAEEFCSKIEKLAKNILKHKLDEEELKKFL-LFNSLEDKEVK--KDLKMQDLKSFDEMKERLKRHDQV 1209          

HSP 2 Score: 28.4906 bits (62), Expect = 4.595e-8
Identity = 11/19 (57.89%), Postives = 16/19 (84.21%), Query Frame = -3
Query:  799 NFIKPPENYEIRANVKDCI 855
            NFIKPPE Y++ ++V+D I
Sbjct: 1055 NFIKPPETYDMDSDVEDFI 1073          
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000023258.1 (SMESG000023258.1)

HSP 1 Score: 47.3654 bits (111), Expect = 4.861e-8
Identity = 44/141 (31.21%), Postives = 71/141 (50.35%), Query Frame = -1
Query:  405 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILR----QSQ*KGIA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKV 797
            ER  ++  I+ EY  KFV A+LS  +TKKY   + TL          LR +F K  + + +L E   Y Q N++         K+ + IL+    + + K    +FN L  K +K  K  K+   K+ ++M ER+K+H++V
Sbjct: 1085 ERFFEMTNIVDEYRSKFVKAFLSINSTKKYELTNETLHYTER-----LRNAFSKNRSLIDDLNEALNYRQGNEAAEEFCSKIEKLAKNILKHKLDEEELKKFL-LFNSLEDKEVK--KDLKMQDLKSFDEMKERLKRHDQV 1217          

HSP 2 Score: 28.4906 bits (62), Expect = 4.861e-8
Identity = 11/19 (57.89%), Postives = 16/19 (84.21%), Query Frame = -3
Query:  799 NFIKPPENYEIRANVKDCI 855
            NFIKPPE Y++ ++V+D I
Sbjct: 1063 NFIKPPETYDMDSDVEDFI 1081          
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000063281.1 (SMESG000063281.1)

HSP 1 Score: 44.669 bits (104), Expect = 4.669e-6
Identity = 33/84 (39.29%), Postives = 42/84 (50.00%), Query Frame = -1
Query:  546 MVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQIL 779
            M I +EY   FV A+LSA   KKY S  + +          L+  FKK M F+ +LQE  KY + ND VN       K  +QIL
Sbjct:    1 MGISEEYREIFVKAFLSANVAKKYESTRKDINYLNR-----LKDVFKKPMKFMDDLQEALKYRKGNDLVNEFCTKIEKFEKQIL 79          
The following BLAST results are available for this feature:
BLAST of SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 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 SMED30003773 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000021279.12.208e-1438.57SMESG000021279.1[more]
SMESG000066474.16.693e-1347.44SMESG000066474.1[more]
SMESG000023258.14.595e-831.21SMESG000023258.1[more]
SMESG000023258.14.861e-831.21SMESG000023258.1[more]
SMESG000063281.14.669e-639.29SMESG000063281.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003773 ID=SMED30003773|Name=SMED30003773|organism=Schmidtea mediterranea sexual|type=transcript|length=1076bp
GTTTTAAAACCGAAAAAAAGAAATCTCTCACGATGCAAAACCACGGTAGT
TAAAATTTATTAATTATTTTTGCTTTGCCAGTTTAAATTGAAAATGAGTT
AAGTTTGGTACGTGTAGTTGATCAAAAAACTAGTTTGATGGAGTTGAAAC
GTTAAGGTGAATTGAATTAAGTTAAATTGAATCCAGGTTTTCCTTAGGGT
GACCTACCAAATTTAAAAATAATGATTTTTGTTTGCGAAGCTCGTAGTTT
ACTAAAATCATGATTAAATCCAGATGAACAAACTTTTTTCCGAAAATAAA
GATTTCTAATTGGATCCAATTGAAAGTATCTTGAATTTTTTACCATAGAT
GCATATTTAATACTTGTTGTCATGGCTGCAACTTGGGAGTTGACCTGATT
AATTTACTTTTTCGTGTTTCTTAATTCTTTCTTACATTTTTTCCATTGTC
TTAAATTTGGTAATTTTTGAAAATTTTCTTCATTTCAATACCTTCCTTGC
CAGGAAATTGAAAATTTATGCAATACCTTTTTATTGAGACTGTCGCAAAA
TTTGTTGATGAACTTTTCTATTAACTGAATCATTGTCTTGGTGATATTTG
AAAACTTCTTGAAGATTATAGACAAAATTCATTTGCTTTTTGAAAGATTT
CCTAAGAATCAAAAATTTAGACACTATAAATAGTTGAAGTGTTCTCGAGT
TGCTNTCATACTTCTTTGTAGCTTTTGCTGATAAATATGCTTATACAAAT
TTCTAACTGTATTCTTTTAAGATGACCATAAGCTTTAAAATTCTTTCAAA
TACAGTCTTTAACGTTGGCTCTGATTTCATAATTCTCTGGCGGTTTAATA
AAATTATCCAATAAAATAACTTGCATCAAGCCATTTACCTTAATTTATTA
ACATTTCAAGTTCCTTTGGAAGTAAAAAAGCTAGCATCTCCAGACTTCAC
ATGCACTCGATTGACTATCCTAAACCGTTTAATAACACGAGGCTTCTGAA
ATCTGATTAAGTTTCAACTGGGTATTGCGAAACGTGCTACCACCTGAGAG
TTTTTTTATTGCTTGCTTGCCAAACG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000043dorsal ventral margin of the whole animal
PLANA:0000070intestinal phagocyte