SMED30004458

Overview
NameSMED30004458
Smed IDSMED30004458
Length (bp)2464
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 SMED30004458 (SMED30004458) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004458 (SMED30004458) 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 SMED30004458 (SMED30004458) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004458 (SMED30004458) 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.
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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
SMED30004458 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001232:97904..100274 -10417
Homology
BLAST of SMED30004458 vs. Planmine SMEST
Match: SMESG000071058.1 (SMESG000071058.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.952e-14
Identity = 23/33 (69.70%), Postives = 27/33 (81.82%), Query Frame = 2
Query: 1877 NHKSISVDKQLVLSERFRRDIAKYHYEAITQNQ 1975
            NH  ISVD+  +LSER RRD+AKYH EAI+QNQ
Sbjct:    6 NHWFISVDQTSLLSERLRRDVAKYHTEAISQNQ 38          

HSP 2 Score: 48.9062 bits (115), Expect = 1.952e-14
Identity = 37/92 (40.22%), Postives = 55/92 (59.78%), Query Frame = 3
Query: 2001 RLIEQIWTRLKDVLKMRIEMEELRVTLKRNGKLLKQANLTIRDNDKEIVQLKLRDKIRSGHVRCGR----------------KDIALSITGP 2228
            R +EQ W R ++V+++R+E++ELR  L +  + L +A+  I + D+EIVQLKL D+IR G VRC R                KDI ++IT P
Sbjct:   48 RCMEQTWMRPEEVVELRVEVDELRSKLAKKEESLAEADQKIGEQDREIVQLKLMDEIRVGLVRCNRKLSIEHEAIVIRNVMEKDIGVAITTP 139          
BLAST of SMED30004458 vs. Planmine SMEST
Match: SMESG000073422.1 (SMESG000073422.1)

HSP 1 Score: 69.707 bits (169), Expect = 7.258e-14
Identity = 49/114 (42.98%), Postives = 62/114 (54.39%), Query Frame = 3
Query: 2007 IEQIWTRLKDVLKMRIEMEELRVTLKRNGKLLKQANLTIRDNDKEIVQLKLRDKIRSGHVRCG-------------RKDIALSITGPKVVQQQNRELSERSKISPNQACAPTPE 2309
            +EQ W R ++    R+EM+ELRV L +  + L QANLTIRD DKEI Q KL+D+IR G VR G             R+D  LSI  PK   +      + +KI   Q  A TPE
Sbjct:   21 MEQTWMRPEEANITRVEMKELRVKLVQTKERLGQANLTIRDRDKEISQFKLKDEIRFGLVRRGSKLSTEQGVVNVIRRDTELSIITPKSAPKIE---PKSAKILSRQTRARTPE 131          
BLAST of SMED30004458 vs. Planmine SMEST
Match: SMESG000001257.1 (SMESG000001257.1)

HSP 1 Score: 55.4546 bits (132), Expect = 3.083e-12
Identity = 29/64 (45.31%), Postives = 41/64 (64.06%), Query Frame = 3
Query: 2001 RLIEQIWTRLKDVLKMRIEMEELRVTLKRNGKLLKQANLTIRDNDKEIVQLKLRDKIRSGHVRC 2192
            R IEQ W   ++V+K+R E+E L + L +  + L QA   IR  D EIV LKL+D+IR+G + C
Sbjct:  701 RRIEQTWLGPEEVIKLRAEIETLNLKLAQKEEALMQAEQKIRTQDSEIVDLKLKDEIRAGLILC 764          

HSP 2 Score: 36.1946 bits (82), Expect = 3.083e-12
Identity = 14/19 (73.68%), Postives = 17/19 (89.47%), Query Frame = 2
Query: 1919 ERFRRDIAKYHYEAITQNQ 1975
            ERFR+D+AKYH EA+ QNQ
Sbjct:  673 ERFRKDVAKYHQEAMVQNQ 691          
BLAST of SMED30004458 vs. Planmine SMEST
Match: SMESG000001257.1 (SMESG000001257.1)

HSP 1 Score: 55.4546 bits (132), Expect = 3.262e-12
Identity = 29/64 (45.31%), Postives = 41/64 (64.06%), Query Frame = 3
Query: 2001 RLIEQIWTRLKDVLKMRIEMEELRVTLKRNGKLLKQANLTIRDNDKEIVQLKLRDKIRSGHVRC 2192
            R IEQ W   ++V+K+R E+E L + L +  + L QA   IR  D EIV LKL+D+IR+G + C
Sbjct:  717 RRIEQTWLGPEEVIKLRAEIETLNLKLAQKEEALMQAEQKIRTQDSEIVDLKLKDEIRAGLILC 780          

HSP 2 Score: 36.1946 bits (82), Expect = 3.262e-12
Identity = 14/19 (73.68%), Postives = 17/19 (89.47%), Query Frame = 2
Query: 1919 ERFRRDIAKYHYEAITQNQ 1975
            ERFR+D+AKYH EA+ QNQ
Sbjct:  689 ERFRKDVAKYHQEAMVQNQ 707          
BLAST of SMED30004458 vs. Planmine SMEST
Match: SMESG000064586.1 (SMESG000064586.1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.104e-10
Identity = 34/73 (46.58%), Postives = 41/73 (56.16%), Query Frame = 3
Query: 2058 MEELRVTLKRNGKLLKQANLTIRDNDKEIVQLKLRDKIRSGHVRCGR----------------KDIALSITGP 2228
            MEE R  L +N + L  AN TI++  KEI QLKL+DKIR G VRCG                 KDIA++IT P
Sbjct:    1 MEEFRAKLAQNEESLAHANQTIKEQGKEITQLKLKDKIREGLVRCGSKLSTEQEAIVIRNVMGKDIAMAITTP 73          
The following BLAST results are available for this feature:
BLAST of SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 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 SMED30004458 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071058.11.952e-1469.70SMESG000071058.1[more]
SMESG000073422.17.258e-1442.98SMESG000073422.1[more]
SMESG000001257.13.083e-1245.31SMESG000001257.1[more]
SMESG000001257.13.262e-1245.31SMESG000001257.1[more]
SMESG000064586.11.104e-1046.58SMESG000064586.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004458 ID=SMED30004458|Name=SMED30004458|organism=Schmidtea mediterranea sexual|type=transcript|length=2464bp
GGTGCAATGAATGTTTTAAGTTTATATTATTTTTTATATTTTTCATGAAC
AAACGAAGATTGATACTGAAATATAATTATTTATAAAAGCATGAAATTAT
ACCTATCGAAGTGGATGTTAGGTTCGTTAGATGTGGTTTACTGTAACCCC
TAACGTGGGATATTACAGAATCTGACTCCAAAGGATTCTACTTACGAGCT
TGTACAATTAGGTTAAGGTGGGATATTACTACTGACCTTGAATAATCCTC
ACTTACATCTCACCTACTTGTTATCCGTTACCATTGTCTATTTTCATCGT
TGGCTTGCATGTGCAGGAAATGGTTAGAAGTCGAAAACCTGGTTCTTATA
GTCGAATCTACAGAATGTAATTACTTGGCAGCAGTAAATGTGTAAGTCAG
CTGAGATCAAGAGATTATCATCCATCGATCCTCGGCAGGATCCCATAAAT
CAATCGCAAGGCGAAGAATGACTGGGCTGGTTTTCGTGTTACTGAATCAA
GCATTCGGACAGATTGGTTGTGGCGTTACAGTTTCATCTCTGCTAGTGGA
GTTTAATGGACTTAGGAGCGAACCCGTAACGAGATCTAAATCTTGTCAGC
ACATGGGAAATCAGTTCTTGACAGTCATAGATTCATTGAGGAATTAATAA
TAGTTTCAAAATATGAGATATAAAGATATTTTTCTTACTAAAGATATTGT
TTCGTATTTCCGAAGTCTGTCCGATGATGAGCTGTTCACCCTCTTCCGAC
GCATTACATCATTGGATGTAGTACAGGTAAAACCTCAGCTTCAAAGTTAT
CTTATTCAGCAACCATACTATAGGTTGTTTTCCCGACCATTTTGATTCGG
ATTAGCTCATAGTAAAAATCTGTTACTATATTTTATTCGTTGTGTTATTC
AATTTGTAACCATTCTCTATGTATACATTATCTAGGTCTTATGAAATGGC
TCTCACCATACGAAAATAACTCCATCACTAAAACTTCCGCCATACAAGCA
CGGATTCGCTTTCTTTAGAAAATTAACAGATTCCATTGTACTGAAATAGT
TTAGGAAAATGTTCGCACTAATTTTGAATTATTTATAATATTGAACAAAT
TCATGTTTTGTTATAGTAACATTAAAATAATTTTAGTACATTTGTATTGA
TCGTTAAAATGAAACCTGAATATGGCATGAACACGATTCATCGGATTGTG
GTGACATAAGCTGTTTAAGACTCACCTTTTGCTGACAAACCGCTTACTAG
TGTTTGTGGAAAACTTATATGAGCCCTAATTTTGGTTGGTTTAGCACGAT
AATGCCTATATACCTTTGACCTGTAACAATGAATATTGAAAAAAACATAA
AATTTAAAAGAAAAAGGAAATAAATAAAAAATAAAATCGAACTTTATCAT
CTAAAACTCGAAAAGTTATAATAAATTAGAAAAAATATATTTTTAATTAA
AATTTTTTTGTTTTACTTACCGCATCTAAATACAAACACGAAAATCGTTG
TTTATAAGTCAGTGCTGGGGGAAAAAATAATTACGTTTTTCTAAAATTTA
TTTACATTTATTATTTAACACGTACTCTTGAAAAAACCATTTTTGACCAC
GTATATTTCATTTCATTATTGAAAGAACTCAAGTAATAATTGTTCTGCTA
TTTTATTATTTTCGCATAATTGTGTTCTAGTTACATTTTTCTTTAACCAT
TATGATTTCATTTGATTACATTACATTAACCATTACATTTGTTCTAATTT
TAAAATGTAGCCATCATTATCGTTTTTTCTTACCTGGCTAGATTAAATAC
CTGTAGCCTTATTTTGTTAAATAAATTCATAATATGATATACGTAGTTCA
AAGTTTTTCTTTTCAAATGCTAATAAAACCATAAAAGTATTTCAGTGGAC
AAACAATTAGTTCTCTCAGAAAGATTTCGACGAGATATCGCAAAATATCA
TTATGAAGCAATCACCCAGAACCAGGGGCAGAAGCTTTAGTGCGTGGTAC
AGACTCATCGAACAGATCTGGACGAGGCTCAAGGATGTGCTGAAGATGCG
GATAGAAATGGAAGAATTGCGGGTTACATTGAAACGAAACGGTAAACTAT
TAAAGCAGGCCAATCTCACAATACGAGATAATGACAAAGAAATCGTGCAG
TTAAAATTGAGAGACAAGATCCGATCCGGACATGTGAGATGCGGAAGAAA
AGATATCGCGTTGTCGATCACAGGCCCGAAAGTAGTCCAACAACAGAATC
GAGAACTGTCCGAAAGGAGCAAAATATCGCCCAATCAAGCGTGCGCGCCA
ACGCCAGAACACCATAAAGACCGCGAGAGTGGTGGGCCACATCCTGCTTT
CCAAAGGATTTTGAGTGGATTTTTGAATGAATTTCCTAACAAAAAATGTG
ATTATGATTCAGTTTAACTTTTGTTGTTATTTAAAAAAATTTTAATAATA
TTAGTTTTATCACG
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protein sequence of SMED30004458-orf-1

>SMED30004458-orf-1 ID=SMED30004458-orf-1|Name=SMED30004458-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=155bp
MKQSPRTRGRSFSAWYRLIEQIWTRLKDVLKMRIEMEELRVTLKRNGKLL
KQANLTIRDNDKEIVQLKLRDKIRSGHVRCGRKDIALSITGPKVVQQQNR
ELSERSKISPNQACAPTPEHHKDRESGGPHPAFQRILSGFLNEFPNKKCD
YDSV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000136whole organism