SMED30014032

Overview
NameSMED30014032
Smed IDSMED30014032
Length (bp)1924
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 SMED30014032 (SMED30014032) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014032 (SMED30014032) 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 SMED30014032 (SMED30014032) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014032 (SMED30014032) 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
SMED30014032 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001690:8612..24533 +9404
Homology
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BLAST of SMED30014032 vs. Planmine SMEST
Match: SMESG000000382.1 (SMESG000000382.1)

HSP 1 Score: 887.1 bits (2291), Expect = 0.000e+0
Identity = 526/530 (99.25%), Postives = 526/530 (99.25%), Query Frame = 2 
Query:   86 MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIXXXXXXXXXXXTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEKKLGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFAXXXXXXXXXXXXXXIFHDQNIPDDLLENSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYHANYSIIEXXXXXXXXXXIDGNEDAKEPLKQNSNVNSVXXXXXXXXXXXXXXXXXXLEKINPEIETPTENPLRLLSNHLRQSISS 1675
            MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIKEKLKKQKDIKTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLSHRSSERKSRSKTGKNVKTNKSSNSKKRKRSLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEK LGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFANPVLENEGLVNNVNIFHDQNIPDDLL NSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYH NYSIIEDL DKDTKTTIDGNEDAKEPLKQNSNVNSVNSETISTTGSSSNTYSNNLEKINPEIETPTENPLRLLSNHLRQSISS
Sbjct:    1 MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIKEKLKKQKDIKTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLSHRSSERKSRSKTGKNVKTNKSSNSKKRKRSLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEKNLGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFANPVLENEGLVNNVNIFHDQNIPDDLLVNSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYHVNYSIIEDLSDKDTKTTIDGNEDAKEPLKQNSNVNSVNSETISTTGSSSNTYSNNLEKINPEIETPTENPLRLLSNHLRQSISS 530
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BLAST of SMED30014032 vs. Planmine SMEST
Match: SMESG000000382.1 (SMESG000000382.1)

HSP 1 Score: 773.081 bits (1995), Expect = 0.000e+0
Identity = 470/478 (98.33%), Postives = 471/478 (98.54%), Query Frame = 2 
Query:  242 STKEYRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIXXXXXXXXXXXTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEKKLGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFAXXXXXXXXXXXXXXIFHDQNIPDDLLENSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYHANYSIIEXXXXXXXXXXIDGNEDAKEPLKQNSNVNSVXXXXXXXXXXXXXXXXXXLEKINPEIETPTENPLRLLSNHLRQSISS 1675
            S  + RCCDCLSKAAPACACHHRDKDLSQNPKIQESCIKEKLKKQKDIKTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLSHRSSERKSRSKTGKNVKTNKSSNSKKRKRSLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEK LGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFANPVLENEGLVNNVNIFHDQNIPDDLL NSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYH NYSIIEDL DKDTKTTIDGNEDAKEPLKQNSNVNSVNSETISTTGSSSNTYSNNLEKINPEIETPTENPLRLLSNHLRQSISS
Sbjct:    4 SITQNRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIKEKLKKQKDIKTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLYLLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLAPLSHRSSERKSRSKTGKNVKTNKSSNSKKRKRSLPTAVNLFQSDTDETHIEKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEKNLGNDRLETEAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILTCYVNNIIQQQASFIRLQSYERSSEMSFANPVLENEGLVNNVNIFHDQNIPDDLLVNSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYHVNYSIIEDLSDKDTKTTIDGNEDAKEPLKQNSNVNSVNSETISTTGSSSNTYSNNLEKINPEIETPTENPLRLLSNHLRQSISS 481
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BLAST of SMED30014032 vs. Planmine SMEST
Match: SMESG000000382.1 (SMESG000000382.1)

HSP 1 Score: 117.857 bits (294), Expect = 8.784e-32
Identity = 58/58 (100.00%), Postives = 58/58 (100.00%), Query Frame = 2 
Query:   86 MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYR 259
            MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYR
Sbjct:    1 MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRKDNSTKEYR 58
[Close]
BLAST of SMED30014032 vs. Planmine SMEST
Match: SMESG000000381.1 (SMESG000000381.1)

HSP 1 Score: 98.5969 bits (244), Expect = 1.944e-21
Identity = 47/47 (100.00%), Postives = 47/47 (100.00%), Query Frame = -3 
Query: 1755 PAFDSSGEVITRNVARVLKESRISSNIYETMEGRQSYKSDQDIYDSI 1895
            PAFDSSGEVITRNVARVLKESRISSNIYETMEGRQSYKSDQDIYDSI
Sbjct:  495 PAFDSSGEVITRNVARVLKESRISSNIYETMEGRQSYKSDQDIYDSI 541
The following BLAST results are available for this feature:
BLAST of SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 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 SMED30014032 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000000382.10.000e+099.25SMESG000000382.1[more]
SMESG000000382.10.000e+098.33SMESG000000382.1[more]
SMESG000000382.18.784e-32100.00SMESG000000382.1[more]
SMESG000000381.11.944e-21100.00SMESG000000381.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014032 ID=SMED30014032|Name=SMED30014032|organism=Schmidtea mediterranea sexual|type=transcript|length=1924bp
GATAATTTGAATTCCGTTATAAAATAATGAATAATTAATATGAACGATTT
ATAAGAAATCGCTAGAAATTAACAATATTTTAGAAATGCTTTCTAGAGAA
AAGGAGGCGAATTATCAAGTAAAAGTAGAGAGAAACAATCACGTATCATC
TAAGCATGACATCAAAAACACTTCAACAAAATTGGTCATGCTAAATCCAA
GCGAAAACAAAATCCGAGAACAAAATCAGCGTAAAGACAATTCGACAAAA
GAATACAGATGCTGTGACTGCCTTTCAAAAGCTGCCCCGGCATGCGCGTG
TCATCATCGTGATAAAGATCTATCTCAGAATCCAAAAATACAGGAAAGTT
GCATTAAAGAAAAATTGAAAAAACAAAAAGACATAAAAACCGGAAGTGGT
AAAAGTAAGGAATTGGGCGAAAGAGAACCAAAATGGCCATCTTTAACAAA
ATCTGAATTATTGGCATTAGATAAAATGAACAGGAAATACCAAATGAAAT
GTGTCGGTGGAAATTGCTGCCATAAAGATCTTTATCTTCTCTCTTCTATT
CCAGCTTTATCTCATCCAGATTTTACTATAGGTCAAAAGCAGTGCTTGTT
ATCTCTCGCAAAAATCTACACCAATGTGAGTCCAGGACCAAGATATTGTT
CACAAAAAGGTCGACAAAACCAATCAAAACTAGCACCGCTATCTCACAGA
AGCAGCGAAAGAAAAAGCAGAAGTAAAACCGGCAAAAATGTCAAAACCAA
TAAAAGTTCAAATTCAAAGAAAAGGAAAAGAAGTTTGCCGACTGCGGTGA
ATTTATTTCAAAGTGATACTGACGAAACCCACATTGAAAAAGGAACAGAA
GACAAGTCAAAACTTAAAGAGTCGCGAAGTGGTTCTTGTGTTGATTCAGT
AACGAAATTAAGCTCGAAACCAGAAATAAGTACTAAAAGTGTTAATTGCG
AGGAAAAAAAGCTCGGTAATGATAGGTTAGAGACAGAAGCTCATGAAAGT
ATCCAATACTCAGACCAATCTTCAAGGAATAGTAATTCGACTCCATTAAT
AGAAACGGAACTTCCTGTTGGCGATGACAGGAATGAGATTTACGAATTGG
AGCTATCCAACACAGATTTAGATTTCATTTTGACCTGCTACGTTAATAAC
ATAATCCAACAGCAAGCGAGTTTTATTCGCCTTCAATCCTATGAAAGAAG
CTCTGAAATGAGCTTTGCGAATCCAGTTCTTGAGAATGAAGGATTAGTGA
ATAATGTTAACATTTTCCATGATCAGAATATCCCAGATGATTTATTAGAG
AATTCAAAGGAAAATCGTTTACCAAGCCAGCGAGAACAAATTATGGATAA
GGAATTCAAAGAAATGATCCATGTCAACGCAGAGTCAGTGAATAAAGATG
AACTAAATGAAACCGATTATCATGCAAATTATTCTATAATTGAAGATCTA
TTAGATAAAGATACGAAAACGACAATTGATGGAAATGAAGATGCTAAAGA
GCCACTCAAACAAAACTCGAATGTGAATAGTGTAAACTCGGAAACAATTT
CTACAACTGGAAGTTCATCAAACACTTATTCCAATAATTTAGAGAAAATA
AACCCAGAAATCGAGACTCCGACAGAAAACCCTCTCAGGCTCCTATCTAA
CCATTTGCGACAATCGATCTCATCATAAATTGCACAGAGAAATTCATATT
TTATTATAAAAAATATTGATAAATGATATGTGATTTGTGTTTTGCTGTCG
ACTAAATAGAGTCATAAATGTCTTGGTCGCTCTTGTAACTTTGCCGCCCT
TCCATTGTTTCATAAATATTCGACGATATTCGGCTTTCTTTGAGGACTCT
TGCAACGTTTCTAGTGATCACTTCACCCGAGGAGTCGAATGCGGGGTTAA
TGTTGTTGTTGTTGCTGTTGTTGT
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protein sequence of SMED30014032-orf-1

>SMED30014032-orf-1 ID=SMED30014032-orf-1|Name=SMED30014032-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=531bp
MLSREKEANYQVKVERNNHVSSKHDIKNTSTKLVMLNPSENKIREQNQRK
DNSTKEYRCCDCLSKAAPACACHHRDKDLSQNPKIQESCIKEKLKKQKDI
KTGSGKSKELGEREPKWPSLTKSELLALDKMNRKYQMKCVGGNCCHKDLY
LLSSIPALSHPDFTIGQKQCLLSLAKIYTNVSPGPRYCSQKGRQNQSKLA
PLSHRSSERKSRSKTGKNVKTNKSSNSKKRKRSLPTAVNLFQSDTDETHI
EKGTEDKSKLKESRSGSCVDSVTKLSSKPEISTKSVNCEEKKLGNDRLET
EAHESIQYSDQSSRNSNSTPLIETELPVGDDRNEIYELELSNTDLDFILT
CYVNNIIQQQASFIRLQSYERSSEMSFANPVLENEGLVNNVNIFHDQNIP
DDLLENSKENRLPSQREQIMDKEFKEMIHVNAESVNKDELNETDYHANYS
IIEDLLDKDTKTTIDGNEDAKEPLKQNSNVNSVNSETISTTGSSSNTYSN
NLEKINPEIETPTENPLRLLSNHLRQSISS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000101muscle cell
PLANA:0002056medial muscle cell
PLANA:0002111X2 cell
PLANA:0003001lateral region of the whole animal
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 467..499
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 187..274
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 473..499
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 245..264
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 305..321
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 187..202
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 292..321