SMED30030540

Overview
NameSMED30030540
Smed IDSMED30030540
Length (bp)741
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 SMED30030540 (SMED30030540) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30030540 (SMED30030540) 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 SMED30030540 (SMED30030540) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30030540 (SMED30030540) 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




SMED30030540

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30030540SMESG000044170.1 SMESG000011277.1 SMESG000011276.1 SMESG000011269.1 SMESG000011261.1 dd_Smed_v4_27_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30030540SMESG000044170.1 SMESG000011277.1 SMESG000011276.1 SMESG000011269.1 SMESG000011261.1 dd_Smed_v6_27_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30030540SMESG000044170.1 SMESG000011277.1 SMESG000011276.1 SMESG000011269.1 SMESG000011261.1 OX_Smed_1.0.00046ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
head regionSMED30030540SMESG000044170.1 SMESG000011277.1 SMESG000011276.1 SMESG000011269.1 SMESG000011261.1 OX_Smed_1.0.05367ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30030540 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002970:15233..15973 +3633
v31.002970:17041..17781 +3588
v31.018726:12759..13499 -3570
v31.012735:12499..13239 +3552
v31.021536:8795..9538 -3550
v31.016548:903..1652 -3473
v31.021754:1194..1967 -3432
Homology
BLAST of SMED30030540 vs. Planmine SMEST
Match: SMESG000011261.1 (SMESG000011261.1)

HSP 1 Score: 220.32 bits (560), Expect = 1.098e-72
Identity = 182/185 (98.38%), Postives = 183/185 (98.92%), Query Frame = 2
Query:  182 MKFAFGFTIFSLVSCFYVDAXXXXXXXXXXXXXXXXXXXXXXXXXXXEASVSAGGADVTAKLGFDLSRFCAGGAGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVDFKANVEASD 736
            MKFAFGFTIFSLVSCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGLSRRGRGGLLDIDSLFSGLPLNGLLGGILNTLD VIPLHLVKTVKHVLN VINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDV+FKANVEASD
Sbjct:    1 MKFAFGFTIFSLVSCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGLSRRGRGGLLDIDSLFSGLPLNGLLGGILNTLDGVIPLHLVKTVKHVLNTVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVNFKANVEASD 185          
BLAST of SMED30030540 vs. Planmine SMEST
Match: SMESG000011276.1 (SMESG000011276.1)

HSP 1 Score: 214.927 bits (546), Expect = 1.264e-70
Identity = 176/185 (95.14%), Postives = 180/185 (97.30%), Query Frame = 2
Query:  182 MKFAFGFTIFSLVSCFYVDAXXXXXXXXXXXXXXXXXXXXXXXXXXXEASVSAGGADVTAKLGFDLSRFCAGGAGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVDFKANVEASD 736
            MKFAFGFTIFSL SCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGL+RRG GG+LDIDSLFSGLPLNGLLGGILNTLDRVIPL LVKTVKHVLNDVIN VQKILRCESNPDKLR+MAKLMYQLQRKGYRFTRLQRRYFKDV+FKAN EASD
Sbjct:    1 MKFAFGFTIFSLASCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGLARRGSGGILDIDSLFSGLPLNGLLGGILNTLDRVIPLGLVKTVKHVLNDVINIVQKILRCESNPDKLRKMAKLMYQLQRKGYRFTRLQRRYFKDVNFKANFEASD 185          
BLAST of SMED30030540 vs. Planmine SMEST
Match: SMESG000011269.1 (SMESG000011269.1)

HSP 1 Score: 214.927 bits (546), Expect = 1.264e-70
Identity = 176/185 (95.14%), Postives = 180/185 (97.30%), Query Frame = 2
Query:  182 MKFAFGFTIFSLVSCFYVDAXXXXXXXXXXXXXXXXXXXXXXXXXXXEASVSAGGADVTAKLGFDLSRFCAGGAGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVDFKANVEASD 736
            MKFAFGFTIFSL SCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGL+RRG GG+LDIDSLFSGLPLNGLLGGILNTLDRVIPL LVKTVKHVLNDVIN VQKILRCESNPDKLR+MAKLMYQLQRKGYRFTRLQRRYFKDV+FKAN EASD
Sbjct:    1 MKFAFGFTIFSLASCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGLARRGSGGILDIDSLFSGLPLNGLLGGILNTLDRVIPLGLVKTVKHVLNDVINIVQKILRCESNPDKLRKMAKLMYQLQRKGYRFTRLQRRYFKDVNFKANFEASD 185          
BLAST of SMED30030540 vs. Planmine SMEST
Match: SMESG000044170.1 (SMESG000044170.1)

HSP 1 Score: 214.157 bits (544), Expect = 2.772e-70
Identity = 171/186 (91.94%), Postives = 175/186 (94.09%), Query Frame = 2
Query:  182 MKFAFGFTIFSLVSCFYVDA-XXXXXXXXXXXXXXXXXXXXXXXXXXXEASVSAGGADVTAKLGFDLSRFCAGGAGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVDFKANVEASD 736
            MKFAFGFTIFSL SCFYVDA L G + GGGG GGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGL+RRG GG+LDID L SGLPLNGLLGGILNTLD VIPLHLVKTVKHVLN VINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDV+FKANVEASD
Sbjct:    1 MKFAFGFTIFSLASCFYVDALLGGILGGGGGEGGLLGGLGGGLLGGGGEASVSAGGADVTAKLGFDLSRFCAGGAGVILGLARRGSGGILDIDRLLSGLPLNGLLGGILNTLDGVIPLHLVKTVKHVLNTVINTVQKILRCESNPDKLRRMAKLMYQLQRKGYRFTRLQRRYFKDVNFKANVEASD 186          
BLAST of SMED30030540 vs. Planmine SMEST
Match: SMESG000011277.1 (SMESG000011277.1)

HSP 1 Score: 116.316 bits (290), Expect = 7.106e-32
Identity = 98/107 (91.59%), Postives = 99/107 (92.52%), Query Frame = 2
Query:  326 ASVSAGGADVTAKLGFDLSRFCAGGAGVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRMAKLMY 646
            ASVSAGGADVTAK GFDLSRFCAGGAGVILGL+RRG GGLLDIDSLFSGLPLNGLL GILNTLD V PL LVKTVKHVLNDVINTVQ ILR ESNPDKLRRMAKLMY
Sbjct:   99 ASVSAGGADVTAKFGFDLSRFCAGGAGVILGLARRGSGGLLDIDSLFSGLPLNGLLCGILNTLDGVKPLGLVKTVKHVLNDVINTVQMILRLESNPDKLRRMAKLMY 205          
The following BLAST results are available for this feature:
BLAST of SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 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 SMED30030540 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000011261.11.098e-7298.38SMESG000011261.1[more]
SMESG000011276.11.264e-7095.14SMESG000011276.1[more]
SMESG000011269.11.264e-7095.14SMESG000011269.1[more]
SMESG000044170.12.772e-7091.94SMESG000044170.1[more]
SMESG000011277.17.106e-3291.59SMESG000011277.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030540 ID=SMED30030540|Name=SMED30030540|organism=Schmidtea mediterranea sexual|type=transcript|length=741bp
TGATAATTGATCACTTACAATTCTCATCAAAAAGTAATCAAGGGGTTCAA
AATGGAATCATAATAATTGACATGTATGTACTCAGTGAAGTGTGACCATT
GAGAATTGCGTTCCTGCAGCATGGCGACATGTGAGGAGTATAAATAGTGA
AATTAAGTTTTAATGAAATTATCAAATAACAATGAAATTTGCTTTTGGTT
TCACAATATTCTCTTTAGTATCATGTTTTTACGTTGATGCTTTGCTTGGA
GGTATTCTAGGTGGAGGAGGAGGAGGAGGTCTTCTTGGAGGATTAGGAGG
AGGTCTTCTGGGTGGAGGTGGAGAAGCTAGTGTAAGTGCCGGAGGCGCTG
ATGTTACTGCAAAATTGGGATTCGATCTTTCAAGGTTCTGTGCTGGTGGA
GCTGGTGTCATTTTAGGTTTATCAAGAAGAGGAAGGGGAGGACTCTTGGA
TATCGATAGCCTTTTTTCTGGATTACCATTAAACGGTTTACTTGGTGGAA
TATTGAACACTCTTGATCGAGTCATACCGCTGCATCTTGTGAAAACTGTT
AAGCACGTTTTGAATGATGTAATCAACACGGTACAAAAGATACTGAGATG
CGAAAGCAATCCTGACAAGTTACGAAGAATGGCGAAATTGATGTATCAGT
TACAACGAAAAGGTTACCGATTTACCAGACTTCAACGAAGATATTTCAAA
GATGTAGATTTTAAAGCGAACGTCGAAGCTTCTGATTAAAT
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protein sequence of SMED30030540-orf-1

>SMED30030540-orf-1 ID=SMED30030540-orf-1|Name=SMED30030540-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=186bp
MKFAFGFTIFSLVSCFYVDALLGGILGGGGGGGLLGGLGGGLLGGGGEAS
VSAGGADVTAKLGFDLSRFCAGGAGVILGLSRRGRGGLLDIDSLFSGLPL
NGLLGGILNTLDRVIPLHLVKTVKHVLNDVINTVQKILRCESNPDKLRRM
AKLMYQLQRKGYRFTRLQRRYFKDVDFKANVEASD*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availablePROSITEPS51257PROKAR_LIPOPROTEINcoord: 1..15
score: 5.0
NoneNo IPR availableTMHMMTMhelixcoord: 7..29