SMED30016249

Overview
NameSMED30016249
Smed IDSMED30016249
Length (bp)1331
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 SMED30016249 (SMED30016249) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016249 (SMED30016249) 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 SMED30016249 (SMED30016249) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30016249 (SMED30016249) 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




SMED30016249

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30016249h1SMcG0003447 dd_Smed_v4_3291_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30016249 vs. Planmine SMEST
Match: SMESG000080837.1 (SMESG000080837.1)

HSP 1 Score: 663.3 bits (1710), Expect = 0.000e+0
Identity = 362/368 (98.37%), Postives = 364/368 (98.91%), Query Frame = 3
Query:   36 MNAKFILFSIAGLGSLMMFYMWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRXXXXXXXXXXXXTDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTIXXXXXXXXXXESQGSKKAKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLLPPGNQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNDKDVKDDVIQSGIDFKNPVKMDMKTD 1139
            MNAKFILFSIAGLGSLMMFYMWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKV SQ SKK+KLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQL PP NQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKN+KDVKDDVIQSGIDFKNPVKMDMKTD
Sbjct:    1 MNAKFILFSIAGLGSLMMFYMWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKVGSQDSKKSKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLFPPENQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNNKDVKDDVIQSGIDFKNPVKMDMKTD 368          
BLAST of SMED30016249 vs. Planmine SMEST
Match: SMESG000080837.1 (SMESG000080837.1)

HSP 1 Score: 619.002 bits (1595), Expect = 0.000e+0
Identity = 342/348 (98.28%), Postives = 344/348 (98.85%), Query Frame = 3
Query:   96 MWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRXXXXXXXXXXXXTDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTIXXXXXXXXXXESQGSKKAKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLLPPGNQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNDKDVKDDVIQSGIDFKNPVKMDMKTD 1139
            MWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKV SQ SKK+KLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQL PP NQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKN+KDVKDDVIQSGIDFKNPVKMDMKTD
Sbjct:    1 MWYSMNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKVGSQDSKKSKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLFPPENQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNNKDVKDDVIQSGIDFKNPVKMDMKTD 348          
BLAST of SMED30016249 vs. Planmine SMEST
Match: SMESG000080837.1 (SMESG000080837.1)

HSP 1 Score: 605.905 bits (1561), Expect = 0.000e+0
Identity = 338/344 (98.26%), Postives = 340/344 (98.84%), Query Frame = 3
Query:  108 MNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRXXXXXXXXXXXXTDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTIXXXXXXXXXXESQGSKKAKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLLPPGNQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNDKDVKDDVIQSGIDFKNPVKMDMKTD 1139
            MNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKV SQ SKK+KLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQL PP NQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKN+KDVKDDVIQSGIDFKNPVKMDMKTD
Sbjct:    1 MNNTVKESQTTEEQYNFRISSLKSEIEAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMDTLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKEDLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPKSPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKVGSQDSKKSKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKDNSQLFPPENQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNNKDVKDDVIQSGIDFKNPVKMDMKTD 344          
The following BLAST results are available for this feature:
BLAST of SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 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 SMED30016249 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000080837.10.000e+098.37SMESG000080837.1[more]
SMESG000080837.10.000e+098.28SMESG000080837.1[more]
SMESG000080837.10.000e+098.26SMESG000080837.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016249 ID=SMED30016249|Name=SMED30016249|organism=Schmidtea mediterranea sexual|type=transcript|length=1331bp
TTTATTATAAACTTGCGATAAATTGAATTTCAAAAATGAATGCAAAATTT
ATATTATTCTCTATTGCTGGTTTGGGTTCATTGATGATGTTTTACATGTG
GTATAGCATGAATAATACTGTCAAAGAATCTCAAACCACAGAGGAACAAT
ATAATTTTAGAATTAGTAGTTTGAAATCTGAAATCGAAGCTGAAAAAAAG
CTAATGGAATCTTTAAGAAAAGACTCTAAGTCTTACTCACAAAATATACA
AGAAAAAACATCACTTGTTGATAAATTGAATAAAAAAGGATTACAATTTG
ATAAAGACAAAGCTAAATTGGAAAAAGATATGGATACATTACGAATGGAT
TTAGACAAGTTAACCAGATCAAGCGAAGAGCAAAAAAAGAAAATAGAAAG
TGAAACAGATGAAATACTCAAAGAGCAAAATGCACAAATAGATAATTTGG
AAAGTGAAATCAAGAAGTTACAAATTGAAAAGGAGGATTTAATGAAAAAA
CAAATTAAAGTGATAAAACCGACGAATATTGCAAAGGTAGATTCCCAGGT
TGATAATGTAATGCAAGGCAAACCTCCTAAAATCAAACAAGCAAAATTAG
AGAAGATCACTTTAGACAAAAAGGAAGATCCGAAATCTCCAATTTCATTA
ATTCCAGAGCATCCAAATTTCAAGGAGGAAAAAAAGCAAGGTGATCAGAA
AAGTGAACCGAAAAATATTTTAAAAATTGATGGGCAAACTATTTCAAATT
CTGTATCAAATAAGAATAAGGTGGAAAGTCAAGGTTCAAAGAAAGCAAAA
TTAAATGAAGACATTCATGTTGAATCGCACTCGGATGCTAAAGATCAAAA
TTCGAAACCTGAAATGTTGAAAGAAAATATCGACTTTAAGCAAGCGCCAA
ATATGTTACCAAATGTACATGCAGTTAAAAAGGACAATTCTCAACTTTTA
CCTCCTGGAAATCAAGTAAAGGATCTAAATGAGTTGAATCCAAAGGATAA
ATCCATTGTACAAGCAAAGCCGGTAAAGGATGAAAATCATCAATTGAAAT
CTCCAAAGAATGATAAAGATGTAAAAGACGATGTCATTCAATCTGGAATA
GATTTCAAAAACCCTGTGAAGATGGATATGAAAACTGATTAAAACATTGC
TAGCTTTCATGTCGCGTTTGTTCAATGATGTTAATAAAAATTGAGATATA
TTTTATCAGGAACAGGCTAGTAAATGTTTATTTCCGCAGAATGTTAATAT
CATTATTATTATTTTTACAAATGTTTTTTTCCATAAATTGTATTTAGTGT
TAATGAAATATATTTTATTTCGAAAAAAAAA
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protein sequence of SMED30016249-orf-1

>SMED30016249-orf-1 ID=SMED30016249-orf-1|Name=SMED30016249-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=369bp
MNAKFILFSIAGLGSLMMFYMWYSMNNTVKESQTTEEQYNFRISSLKSEI
EAEKKLMESLRKDSKSYSQNIQEKTSLVDKLNKKGLQFDKDKAKLEKDMD
TLRMDLDKLTRSSEEQKKKIESETDEILKEQNAQIDNLESEIKKLQIEKE
DLMKKQIKVIKPTNIAKVDSQVDNVMQGKPPKIKQAKLEKITLDKKEDPK
SPISLIPEHPNFKEEKKQGDQKSEPKNILKIDGQTISNSVSNKNKVESQG
SKKAKLNEDIHVESHSDAKDQNSKPEMLKENIDFKQAPNMLPNVHAVKKD
NSQLLPPGNQVKDLNELNPKDKSIVQAKPVKDENHQLKSPKNDKDVKDDV
IQSGIDFKNPVKMDMKTD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 92..155
NoneNo IPR availableCOILSCoilCoilcoord: 43..70
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 183..227
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 314..352
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 248..281
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 171..368
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 228..247
NoneNo IPR availableTMHMMTMhelixcoord: 5..24