SMED30030201

Overview
NameSMED30030201
Smed IDSMED30030201
Length (bp)2177
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 SMED30030201 (SMED30030201) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030201 (SMED30030201) 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 SMED30030201 (SMED30030201) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030201 (SMED30030201) 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




SMED30030201

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30030201h1SMcG0007114 SmedASXL_017369SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30030201 SmedASXL_077222SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030201 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001068:3260..5442 -10106
v31.007059:12900..15083 -9781
v31.000463:122195..124356 -9577
v31.015748:1..7756 +8225
Homology
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000030881.1 (SMESG000030881.1)

HSP 1 Score: 370.163 bits (949), Expect = 1.914e-145
Identity = 196/211 (92.89%), Postives = 201/211 (95.26%), Query Frame = 1
Query: 1054 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRXXXXXXXXXXXXXXAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNSYEF 1686
            MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKKPIPIKAVTVSATSKDLCQSNCG IR KKRIG SDDVDLDSESICGDYKYPVLNDSAKI+FSNIPM+KKSVSTN  DDTYLVN D+ELSDL+F  RPPQTI D+DYLHNLQ EVNSYEF
Sbjct:    1 MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKKPIPIKAVTVSATSKDLCQSNCGPIRSKKRIGFSDDVDLDSESICGDYKYPVLNDSAKISFSNIPMLKKSVSTNT-DDTYLVNNDEELSDLEFSFRPPQTINDDDYLHNLQKEVNSYEF 210          

HSP 2 Score: 121.709 bits (304), Expect = 1.914e-145
Identity = 67/91 (73.63%), Postives = 75/91 (82.42%), Query Frame = 2
Query: 1820 NCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQKVK 2092
            NCEN+SNRN VVLIS+NAIPT F KSNLL+T LENETT AEITLSNESRNI  TAGF L QTPA+L ++D KL N++ I   IMNNDQKVK
Sbjct:  256 NCENISNRN-VVLISENAIPTSFDKSNLLRTLLENETTSAEITLSNESRNIVSTAGFDLTQTPASLTNTDLKLSNFN-ISPTIMNNDQKVK 344          

HSP 3 Score: 67.0106 bits (162), Expect = 1.914e-145
Identity = 31/43 (72.09%), Postives = 36/43 (83.72%), Query Frame = 3
Query: 1692 EMSETEMNNYHQK*FASKNVNPKLSWKCSTCSSGNSNHSLECQ 1820
            ++SE EMNNYHQK F SKN+N K+SWKCSTCSS NS  SLEC+
Sbjct:  213 KISENEMNNYHQKLFGSKNINSKVSWKCSTCSSENSYDSLECK 255          
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000003624.1 (SMESG000003624.1)

HSP 1 Score: 261.922 bits (668), Expect = 3.551e-77
Identity = 149/183 (81.42%), Postives = 155/183 (84.70%), Query Frame = 1
Query: 1129 MAIRHSKDFISSPAKKILEKLDKLTTPITEADKLASLLVRVKAPINNVDRLKASNPYSRXXXXXXXXXXXXXXAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 1677
            M IR++K  +SSP K ILEKLDK TT ITEADKLA+  +              SNPYSRP PPIGRKKPIPIKAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESI G+YKYPVLNDSAKITFSNIPMVKKSVSTN   DTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS
Sbjct:    1 MPIRYTKVVVSSPGKNILEKLDKFTTAITEADKLAASFL-------------TSNPYSRPPPPIGRKKPIPIKAVTVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESIFGNYKYPVLNDSAKITFSNIPMVKKSVSTNTAGDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 170          

HSP 2 Score: 161.77 bits (408), Expect = 1.972e-41
Identity = 80/91 (87.91%), Postives = 83/91 (91.21%), Query Frame = 2
Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQK 2086
            + N +   N NAVVLISDNAIPTGFGKSNLL+TPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSD KLPNYSTIESAIMNND K
Sbjct:  161 LHNLQGEVNSNAVVLISDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDHK 251          
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000002138.1 (SMESG000002138.1)

HSP 1 Score: 199.904 bits (507), Expect = 1.113e-59
Identity = 101/113 (89.38%), Postives = 104/113 (92.04%), Query Frame = 2
Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWSFG 2152
            + N +   N NAVVL SDNAIPTGFGKSNLL+TPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSD KLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWS G
Sbjct:   80 LHNLQGEVNSNAVVLKSDNAIPTGFGKSNLLRTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDIKLPNYSTIESAIMNNDQKVKIPNSQIFSTIQISSLVWSSG 192          

HSP 2 Score: 157.918 bits (398), Expect = 2.726e-44
Identity = 74/75 (98.67%), Postives = 74/75 (98.67%), Query Frame = 1
Query: 1453 ESICGDYKYPVLNDSAKITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 1677
            ESICGDYKYPVLNDSAKI FSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS
Sbjct:   15 ESICGDYKYPVLNDSAKINFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLHNLQGEVNS 89          
BLAST of SMED30030201 vs. Planmine SMEST
Match: SMESG000004159.1 (SMESG000004159.1)

HSP 1 Score: 167.162 bits (422), Expect = 7.551e-49
Identity = 83/91 (91.21%), Postives = 85/91 (93.41%), Query Frame = 2
Query: 1814 MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNESRNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQK 2086
            MPNCENMSNRNAVVLI DNAIPTG GKSNLL+TPLENETTCAEI LSNESRNIAFTAGF LAQTPA+L DSD KLPNYSTIESAIMNNDQK
Sbjct:    1 MPNCENMSNRNAVVLIFDNAIPTGLGKSNLLRTPLENETTCAEIALSNESRNIAFTAGFDLAQTPASLTDSDIKLPNYSTIESAIMNNDQK 91          
The following BLAST results are available for this feature:
BLAST of SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 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 SMED30030201 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000030881.11.914e-14592.89SMESG000030881.1[more]
SMESG000003624.13.551e-7781.42SMESG000003624.1[more]
SMESG000002138.11.113e-5989.38SMESG000002138.1[more]
SMESG000004159.17.551e-4991.21SMESG000004159.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030201 ID=SMED30030201|Name=SMED30030201|organism=Schmidtea mediterranea sexual|type=transcript|length=2177bp
GTGCGGCGTCGGTGCTGCGGCAAGGGGTTGTGAATCCGCCAAAGATAAGC
TTCGTAACTGAGATTGATCTGACCTGGACTCACAGTTGGGTTAAGCTAAC
TGCCGTTAGAAGGTCTCTGCGCGTTTTCTCTTTCTTTGTCCTTATCTTAT
TTATTATTGCTTGATCTTTAGGTGATGTCTTCGCTTTTACTTAGTTTTCA
GTAATGATTCATTTACGAGGAGCGTTAGTGAATTAGGACGCAAAAAAATT
TATTAAATTAATTATGCTTTATTCTAAAGCTAGTACCGCTTTCTCGTGGT
AAACATTGTTAATTTACTATTATAATGTATTTATAATAAACGGAGATGGA
CAAAACATAAATGAATTTATTTGACCGACAACGTTATAACATTCTCATCA
CAGCATTCCGGCTCTCAGAATGGGATTTTGAGGTATCTAGATTTTTCCGG
ACTTGGGCTTTCCTTGCTGCAACACGGGTTTTGATATTTCTGAACTTCAA
TCTCCATAGTTAGATTATGTAATTAAATCATAACTATTACATCATATTGT
TACCGCATTTACTAAACATTTAAATAAAACGGCTAAAAATAAAGTAACAC
TAATTTTTCTATTTTCTATTTATTACTACTTCATATTTTTAATTTTCTAC
TTTCTATTCTGTCATTTTTCAAAAGCTGAGCGACTCTTTCTCAAGCATAT
TTCCTTTTAATTCAACTACTAGAGAAGACATATCTAATGTTTCTTTTGAT
AGAAATTTGTCGCCGATTACAAGTTCTAATCGACGACTAGCATCCGAAGC
ATTTGGTAGAGACGATGATGAATTAAGAATAAAGAGAGCAAGACTGCATT
ATGACCTTAAATCCTTACCGACATCAAGGATAGTGAAACCAATTACTACT
CACTTACCAGATCGCTATAATGCGTACAATAATAATTTTAATGATACTGC
TTCAGATTTCAGTGATACAAGCAATGTATCCGTCTCGACGAGTGGTGTAT
CATCGCTTCATCCACGTTCATCAAAAAGGTTTAATTTAGGACTTGTGGAA
GATATGCAAATACAGAATAATTATAAATATCCAAGAAATTTAAACGTGTC
GCAAAAACCAAATTCTTCAGTTTCACACATGGCAATCAGACATTCTAAAG
ATTTTATTAGTTCACCAGCCAAAAAAATTTTAGAAAAGCTTGATAAACTT
ACTACTCCAATAACGGAGGCGGATAAATTGGCAAGTCTATTGGTCAGGGT
AAAGGCACCAATTAATAATGTCGACAGGCTAAAGGCTTCTAATCCGTATA
GTAGACCAACTCCTCCTATCGGTAGAAAAAAACCAATACCGATTAAAGCT
GTGACGGTATCAGCAACATCTAAAGATCTTTGTCAAAGTAATTGTGGTCG
TATTCGTTGGAAAAAACGTATTGGGGTTTCAGATGATGTTGATTTGGATT
CAGAATCCATTTGTGGTGACTATAAATATCCTGTTTTAAACGATTCTGCA
AAAATAACTTTCTCAAATATTCCCATGGTAAAGAAGTCTGTGTCGACAAA
TAGAGAGGATGATACATATTTAGTGAATAAGGACGATGAATTGTCCGATT
TGCAATTTCCTTTGAGGCCGCCACAAACCATTACTGATGAGGACTATTTG
CACAACTTACAAGGAGAAGTCAATTCGTATGAATTCAAATGGAAATGAGC
GAAACTGAAATGAATAATTATCACCAGAAATGATTTGCTAGTAAAAATGT
GAATCCTAAACTCTCATGGAAATGTAGCACTTGCTCCTCAGGAAACTCTA
ATCATTCACTCGAATGCCAAATTGCGAAAACATGTCAAATAGAAATGCCG
TCGTCCTCATATCCGACAATGCCATTCCTACCGGTTTTGGCAAATCAAAT
CTCCTGAAAACACCTTTAGAAAACGAAACCACTTGTGCAGAAATCACTTT
ATCGAACGAGTCAAGAAACATTGCTTTTACGGCTGGTTTTGTACTCGCAC
AAACGCCCGCAAATTTGGCGGATAGCGATAAAAAATTACCGAATTATAGC
ACTATTGAATCAGCAATTATGAATAATGATCAAAAGGTGAAAATTCCAAA
TTCTCAAATATTTTCAACAATACAAATTTCTAGTCTTGTTTGGTCTTTTG
GTTGTTAATAATATTTATGAATTTTTA
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protein sequence of SMED30030201-orf-1

>SMED30030201-orf-1 ID=SMED30030201-orf-1|Name=SMED30030201-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=215bp
MQIQNNYKYPRNLNVSQKPNSSVSHMAIRHSKDFISSPAKKILEKLDKLT
TPITEADKLASLLVRVKAPINNVDRLKASNPYSRPTPPIGRKKPIPIKAV
TVSATSKDLCQSNCGRIRWKKRIGVSDDVDLDSESICGDYKYPVLNDSAK
ITFSNIPMVKKSVSTNREDDTYLVNKDDELSDLQFPLRPPQTITDEDYLH
NLQGEVNSYEFKWK*
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protein sequence of SMED30030201-orf-2

>SMED30030201-orf-2 ID=SMED30030201-orf-2|Name=SMED30030201-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
MPNCENMSNRNAVVLISDNAIPTGFGKSNLLKTPLENETTCAEITLSNES
RNIAFTAGFVLAQTPANLADSDKKLPNYSTIESAIMNNDQKVKIPNSQIF
STIQISSLVWSFGC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell