SMED30027735

Overview
NameSMED30027735
Smed IDSMED30027735
Length (bp)857
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 SMED30027735 (SMED30027735) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027735 (SMED30027735) 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 SMED30027735 (SMED30027735) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027735 (SMED30027735) 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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Alignments
SMED30027735 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000069:266915..267786 +3103
v31.009512:5610..6402 -2931
v31.008150:22432..23323 +2746
v31.000646:91047..91938 -2656
v31.001610:1527..2383 -2632
v31.003089:52173..53025 +2452
v31.000239:111140..111895 +2448
v31.005945:5561..6360 -2292
Homology
BLAST of SMED30027735 vs. Planmine SMEST
Match: SMESG000074465.1 (SMESG000074465.1)

HSP 1 Score: 169.859 bits (429), Expect = 5.729e-53
Identity = 80/105 (76.19%), Postives = 93/105 (88.57%), Query Frame = 2
Query:  218 IFIVIEMEPLKILQTELTHARKTNKNLYDQIVQLSREVQQTKVTWVDPKKAKLLYQRLTVAQKGFAEEKQLTQSLRTQIRGLEVALSACQEGTAVTYPLIFAPAQ 532
            +F++ EMEPL+ILQTEL  ARK NK+L+DQIVQL+ EVQQTK  W++PKK KLLYQRLT AQKG+AEE+QL Q LRTQI+GLEVALSACQEG AVTYPL+FAPAQ
Sbjct:    1 MFVITEMEPLQILQTELERARKINKDLHDQIVQLTMEVQQTKDVWMEPKKVKLLYQRLTAAQKGWAEERQLVQGLRTQIKGLEVALSACQEGAAVTYPLVFAPAQ 105          
BLAST of SMED30027735 vs. Planmine SMEST
Match: SMESG000026161.1 (SMESG000026161.1)

HSP 1 Score: 164.851 bits (416), Expect = 5.917e-51
Identity = 76/105 (72.38%), Postives = 89/105 (84.76%), Query Frame = 2
Query:  218 IFIVIEMEPLKILQTELTHARKTNKNLYDQIVQLSREVQQTKVTWVDPKKAKLLYQRLTVAQKGFAEEKQLTQSLRTQIRGLEVALSACQEGTAVTYPLIFAPAQ 532
            +F++  MEPL+ILQ EL H R+ NKNL DQ +QL+REVQQ K TW+DPKK + LYQRLT AQKG+AEEKQL QSL+ QI+GLEVALSACQEG AVTYPL+FAPAQ
Sbjct:    1 MFVIAAMEPLQILQKELFHVRQANKNLLDQAIQLTREVQQVKATWMDPKKVRSLYQRLTAAQKGWAEEKQLIQSLKIQIKGLEVALSACQEGAAVTYPLVFAPAQ 105          
BLAST of SMED30027735 vs. Planmine SMEST
Match: SMESG000019745.1 (SMESG000019745.1)

HSP 1 Score: 175.637 bits (444), Expect = 1.442e-50
Identity = 85/105 (80.95%), Postives = 95/105 (90.48%), Query Frame = 2
Query:  218 IFIVIEMEPLKILQTELTHARKTNKNLYDQIVQLSREVQQTKVTWVDPKKAKLLYQRLTVAQKGFAEEKQLTQSLRTQIRGLEVALSACQEGTAVTYPLIFAPAQ 532
            +FI+  MEPL+ILQTELTHAR+ NKNL++QI+QL REVQQTK TWVDPKKAK LYQRLT AQK +AEEKQLTQSLRTQI+ LEVALSACQEG AVTYPL+FAPAQ
Sbjct:    1 MFIIAAMEPLQILQTELTHARQANKNLHNQIIQLPREVQQTKATWVDPKKAKSLYQRLTAAQKVWAEEKQLTQSLRTQIKRLEVALSACQEGAAVTYPLVFAPAQ 105          
BLAST of SMED30027735 vs. Planmine SMEST
Match: SMESG000069193.1 (SMESG000069193.1)

HSP 1 Score: 166.007 bits (419), Expect = 3.071e-49
Identity = 75/107 (70.09%), Postives = 92/107 (85.98%), Query Frame = 2
Query:  212 NLIFIVIEMEPLKILQTELTHARKTNKNLYDQIVQLSREVQQTKVTWVDPKKAKLLYQRLTVAQKGFAEEKQLTQSLRTQIRGLEVALSACQEGTAVTYPLIFAPAQ 532
            N   I++EM+P+K+LQTELTHAR+ NK L+DQ+VQ+ RE+QQ K TW++PK+ K LYQ+L  AQKG+AEEKQL Q L+TQIRGLEVALSACQEG AVTYPL+FAPAQ
Sbjct:  169 NSPLIILEMDPVKLLQTELTHARQANKKLHDQLVQIVREIQQIKATWIEPKRVKPLYQKLATAQKGWAEEKQLVQGLKTQIRGLEVALSACQEGAAVTYPLVFAPAQ 275          
BLAST of SMED30027735 vs. Planmine SMEST
Match: SMESG000061026.1 (SMESG000061026.1)

HSP 1 Score: 160.229 bits (404), Expect = 3.937e-49
Identity = 72/105 (68.57%), Postives = 88/105 (83.81%), Query Frame = 2
Query:  218 IFIVIEMEPLKILQTELTHARKTNKNLYDQIVQLSREVQQTKVTWVDPKKAKLLYQRLTVAQKGFAEEKQLTQSLRTQIRGLEVALSACQEGTAVTYPLIFAPAQ 532
            +F++  ME  + LQTEL HAR+ NKNL DQ++QL+REVQQ K TW DPKK K LY RLT AQKG+A+E+QL QSL+TQ++GLEVALSACQEG A+TYPL+FAPAQ
Sbjct:    1 MFVIAAMESTQPLQTELAHARRANKNLLDQVIQLTREVQQIKSTWSDPKKTKALYLRLTAAQKGWADERQLNQSLKTQVKGLEVALSACQEGAAITYPLVFAPAQ 105          
The following BLAST results are available for this feature:
BLAST of SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 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 SMED30027735 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074465.15.729e-5376.19SMESG000074465.1[more]
SMESG000026161.15.917e-5172.38SMESG000026161.1[more]
SMESG000019745.11.442e-5080.95SMESG000019745.1[more]
SMESG000069193.13.071e-4970.09SMESG000069193.1[more]
SMESG000061026.13.937e-4968.57SMESG000061026.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027735 ID=SMED30027735|Name=SMED30027735|organism=Schmidtea mediterranea sexual|type=transcript|length=857bp
CTACTCAGCTGAGGAAGGGGTGAAGAAATTTTTTGAAGAACCCTGATCCC
ACTGATCTGTGGGTTATGGACCTTTTAGTTTTGCGTGAATGTTATTACAA
TAAATAATTTGTTATTTAAGATTTTCATTTTTACTCGTTTCTTAGTGTAA
CTTCGCAAATTTATGTTTTAAATTAACTTTATACTTAGTAATTCTGAATT
TGGTGGAAAGGAATTTAATTTTCATTGTTATAGAAATGGAACCCCTGAAA
ATATTACAAACAGAACTAACACACGCACGGAAAACCAATAAGAACCTTTA
CGACCAGATTGTTCAACTATCCCGCGAGGTTCAGCAGACAAAAGTCACAT
GGGTGGACCCAAAGAAGGCCAAATTACTGTATCAAAGACTTACAGTAGCC
CAAAAGGGATTTGCGGAAGAAAAACAACTAACTCAAAGCCTAAGGACACA
AATAAGGGGACTGGAGGTTGCACTATCTGCCTGCCAAGAAGGGACAGCTG
TAACTTACCCCCTCATCTTTGCTCCTGCCCAATAGCCTATCGAGAGGCGG
TAGCAACTCCAAAAACGACACCAACAACGCACAGTTATCGTCCTGGACGA
AAGAAGCGGGCAAAACGCCGAGCCGCTCGAATATTGAAAAACCCGCAACG
AACACACTAAAATCCTCCATTACGATACGTAGCCACTTGTTTTATTTTTA
ATATATAATTGTCGATTTTTTTTTGTTTTATGATGAACTCAAACGATAAA
ATCTACGACACAAAGGGGACCTAATAATCTAAAGCGAGCACAAATTTTCC
AACGACAGCTCGTTGAACCCAGAGATCGTTCGGGCAATTACAGCATTAGT
AATAGCG
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protein sequence of SMED30027735-orf-1

>SMED30027735-orf-1 ID=SMED30027735-orf-1|Name=SMED30027735-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
MGGPKEGQITVSKTYSSPKGICGRKTTNSKPKDTNKGTGGCTICLPRRDS
CNLPPHLCSCPIAYREAVATPKTTPTTHSYRPGRKKRAKRRAARILKNPQ
RTH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia