SMED30006089

Overview
NameSMED30006089
Smed IDSMED30006089
Length (bp)664
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast 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 SMED30006089 (SMED30006089) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006089 (SMED30006089) in cells (dots) of each of the 12 neoblast clusters.

 

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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.
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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
SMED30006089 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001767:27222..27914 -2945
Homology
BLAST of SMED30006089 vs. Planmine SMEST
Match: SMESG000038817.1 (SMESG000038817.1)

HSP 1 Score: 43.8986 bits (102), Expect = 3.307e-11
Identity = 37/98 (37.76%), Postives = 49/98 (50.00%), Query Frame = -2
Query:  250 SRWPKQA*QGTALRQINMETEL*ARLSGREAALRICIIPLHHL-TKPANGLNRTTGK--LEISSMPVNSPNPTMPSALSRHKPKKIENVANVDGLSKL 534
            S+W   A Q  ALR+I  E +L ARL  R  A R+ IIP HHL T P +          +E+++ P N      P+A S  K K I+ V  V  L+ L
Sbjct:   72 SQWITVADQSAALREIFTEKKLQARLPSRNMAQRLDIIPTHHLPTNPEDSRTNYNANVLVELATQP-NVNRRHKPTAASNPKSKVIQRVVLVTTLTCL 168          

HSP 2 Score: 41.9726 bits (97), Expect = 3.307e-11
Identity = 22/35 (62.86%), Postives = 23/35 (65.71%), Query Frame = -3
Query:  522 LQQNYEKLKGTWSSREATKALYKKINRLLYCRDGL 626
            L + Y KLKGTW S EATK LYKKI RL    D L
Sbjct:   32 LPEKYNKLKGTWWSPEATKELYKKIMRLSQALDDL 66          
BLAST of SMED30006089 vs. Planmine SMEST
Match: SMESG000033008.1 (SMESG000033008.1)

HSP 1 Score: 47.3654 bits (111), Expect = 3.587e-11
Identity = 21/42 (50.00%), Postives = 29/42 (69.05%), Query Frame = -3
Query:  522 FEVHYTQLQQNYEKLKGTWSSREATKALYKKINRLLYCRDGL 647
             E  +T L+  Y+K+KGTWS  EAT+ LY+K++RL   RD L
Sbjct:   27 LERDFTALKSKYQKIKGTWSPPEATRNLYQKLSRLSRARDDL 68          

HSP 2 Score: 38.1206 bits (87), Expect = 3.587e-11
Identity = 23/46 (50.00%), Postives = 27/46 (58.70%), Query Frame = -2
Query:  388 QGTALRQINMETEL*ARLSGREAALRICIIPLHHL-----TKPANG 510
            Q  ALRQI  E EL ARLS R  A  I IIP+ +L     + P+NG
Sbjct:   82 QSAALRQIFTENELRARLSSRSWAQEINIIPVQNLPINPGSLPSNG 127          
BLAST of SMED30006089 vs. Planmine SMEST
Match: SMESG000021151.1 (SMESG000021151.1)

HSP 1 Score: 43.1282 bits (100), Expect = 5.485e-11
Identity = 41/122 (33.61%), Postives = 54/122 (44.26%), Query Frame = -2
Query:  166 QGTALRQINMETEL*ARLSGREAALRICIIPLHHLTKPANGLNRTTGKLEISSMPVNSPNPTMPSALSRHKP------KKIENVANVDGLSKLLS-ELEAFKESLSCQSTTRTQNGYNCSLI 510
            Q  ALRQI  E EL ARL  R  A +I IIP HHL  P N  N+   +        ++P   +  A  RHKP      ++     N   L+ L S E     E L   +  R  +GY+  +I
Sbjct:   80 QSAALRQIFTEKELQARLPSRNLAQQINIIPAHHL--PTNAENQAINQDN------STPEDGISHANRRHKPNRNRRQRQRRRAENTLLLANLRSDEYPDVTEVLDSTTIERAISGYDKEII 193          

HSP 2 Score: 41.5874 bits (96), Expect = 5.485e-11
Identity = 23/56 (41.07%), Postives = 30/56 (53.57%), Query Frame = -3
Query:  522 RTPFEVHYTQ-----------LQQNYEKLKGTWSSREATKALYKKINRLLYCRDGL 656
            R P+ V   Q           +++ YEK+KGTW S +ATK L+KKI  L   RD L
Sbjct:   11 RAPYAVAMNQRLESLERENFIIREKYEKIKGTWCSPDATKELHKKITSLSRDRDDL 66          
BLAST of SMED30006089 vs. Planmine SMEST
Match: SMESG000041408.1 (SMESG000041408.1)

HSP 1 Score: 50.447 bits (119), Expect = 6.440e-11
Identity = 26/47 (55.32%), Postives = 31/47 (65.96%), Query Frame = -3
Query:  507 FEVHYTQLQQNYEKLKGTWSSREATKALYKKINRLLYCRDGLSRPSR 647
             E  +T LQ  Y+KLKGTWSS E+TK L++KI RL   RD L   SR
Sbjct:   27 LEKDHTVLQAKYQKLKGTWSSPESTKKLFQKIARLTRARDELIIESR 73          

HSP 2 Score: 33.8834 bits (76), Expect = 6.440e-11
Identity = 21/40 (52.50%), Postives = 24/40 (60.00%), Query Frame = -2
Query:  391 QGTALRQINMETEL*ARLSGREAALRICIIPLHHLTKPAN 510
            Q TALR+I  E EL ARL G   A  + IIP  HL  P+N
Sbjct:   82 QSTALRRIFTEAELRARLPGCSLAQSLDIIPAQHL--PSN 119          
BLAST of SMED30006089 vs. Planmine SMEST
Match: SMESG000032225.1 (SMESG000032225.1)

HSP 1 Score: 43.8986 bits (102), Expect = 8.706e-11
Identity = 22/39 (56.41%), Postives = 25/39 (64.10%), Query Frame = -3
Query:  498 YEKLKGTWSSREATKALYKKINRLLYCRDGLSRPSRVPR 614
            YEK+KGTW S EATK LYK I R+   RD L   +R  R
Sbjct:   30 YEKMKGTWCSPEATKELYKNITRISRARDDLIVENRTQR 68          

HSP 2 Score: 40.4318 bits (93), Expect = 8.706e-11
Identity = 28/71 (39.44%), Postives = 36/71 (50.70%), Query Frame = -2
Query:  289 ALRQINMETEL*ARLSGREAALRICIIPLHHLTKPANGLNRTTGKLEISSMPVNSPNPTMPSALSRHKPKK 501
            ALRQ+  E EL ARL GR  A ++ II +HHL  P    NR    +  + M      P +P    +HKP K
Sbjct:   77 ALRQLFTEKELQARLPGRSTAQQLNIISVHHL--PVYSSNRIERDVTNAVM----TRPVLPICNRKHKPNK 141          
The following BLAST results are available for this feature:
BLAST of SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 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 SMED30006089 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000038817.13.307e-1137.76SMESG000038817.1[more]
SMESG000033008.13.587e-1150.00SMESG000033008.1[more]
SMESG000021151.15.485e-1133.61SMESG000021151.1[more]
SMESG000041408.16.440e-1155.32SMESG000041408.1[more]
SMESG000032225.18.706e-1156.41SMESG000032225.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006089 ID=SMED30006089|Name=SMED30006089|organism=Schmidtea mediterranea sexual|type=transcript|length=664bp
CATCGATCCGCCCTAGTCCACAGTATCCCTCGATAAGCCAGATTGAATAG
TCACTTCCAGTCGGGATGGCAGAAGTACATTCATCCGATCTACGGATGCG
CTAAGATTTACGGCTTGTTTCCAAGGACTCACTGGTCATCAGGTACCATG
CCCGATATTGGATCGGATTAGAGAGCAATTATAACCATTCTGCGTACGGG
TGGTTGACTGGCACGATAGAGATTCCTTGAAAGCTTCCAGCTCTGAGAGC
AGCTTGCTCAATCCGTCGACGTTCGCGACGTTTTCGATTTTTTTGGGCTT
GTGCCGAGAGAGAGCACTTGGCATTGTAGGATTAGGGCTATTTACTGGCA
TTGATGATATTTCCAGTTTTCCTGTTGTTCGATTGAGCCCATTTGCTGGT
TTTGTCAGATGATGTAGAGGAATGATACATATTCGCAAAGCCGCTTCTCG
GCCAGACAAACGGGCCTAGAGTTCCGTCTCCATATTTATTTGCCTCAGCG
CGGTACCCTGCTAGGCCTGCTTAGGCCATCTCGACAATAGAGAAGTCTAT
TGATCTTTTTGTAGAGCGCCTTGGTGGCTTCCCGGGAACTCCACGTTCCC
TTTAATTTCTCATAATTCTGCTGCAGTTGAGTGTAATGCACTTCAAACGG
GGTGCGAGGATCGA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
Vocabulary: INTERPRO
TermDefinition
IPR000299FERM_domain
Vocabulary: cellular component
TermDefinition
GO:0005856cytoskeleton