SMED30028170

Overview
NameSMED30028170
Smed IDSMED30028170
Length (bp)1608
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 SMED30028170 (SMED30028170) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028170 (SMED30028170) 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 SMED30028170 (SMED30028170) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028170 (SMED30028170) 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



SMED30028170

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
X1 cellSMED30028170SMESG000037796.1 SmedASXL_014985SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30028170SMESG000037796.1 SmedASXL_014985SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
protonephridiaSMED30028170SMESG000037796.1 SMESG000057565.1 SMESG000057564.1 dd_Smed_v4_2842_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30028170SMESG000037796.1 SMESG000057565.1 SMESG000057564.1 dd_Smed_v4_2842_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30028170SMESG000057565.1 SMESG000057564.1 SMESG000037796.1 dd_Smed_v6_2842_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cholinergic neuronSMED30028170SMESG000057565.1 SMESG000057564.1 SMESG000037796.1 dd_Smed_v6_2842_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028170 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009509:1135..2742 -7986
Homology
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BLAST of SMED30028170 vs. Ensembl Mouse
Match: Sdsl (serine dehydratase-like [Source:MGI Symbol;Acc:MGI:2182607])

HSP 1 Score: 51.2174 bits (121), Expect = 1.899e-6
Identity = 28/59 (47.46%), Postives = 40/59 (67.80%), Query Frame = 3 
Query:  135 LDEQNCLVEPACGASLSALYNGTLDQM-AECR--ECDLNIVVVVCGGRCIDVTSLIEMK 302
            LD++  LVEPACGA+L+A+Y+G L ++ AE R      ++VV+VCGG  I    L E+K
Sbjct:  265 LDDERMLVEPACGAALAAIYSGILWRLQAEGRLSSALASVVVIVCGGNNISSQQLQELK 323
[Close]
BLAST of SMED30028170 vs. Ensembl Mouse
Match: Sdsl (serine dehydratase-like [Source:MGI Symbol;Acc:MGI:2182607])

HSP 1 Score: 51.2174 bits (121), Expect = 1.899e-6
Identity = 28/59 (47.46%), Postives = 40/59 (67.80%), Query Frame = 3 
Query:  135 LDEQNCLVEPACGASLSALYNGTLDQM-AECR--ECDLNIVVVVCGGRCIDVTSLIEMK 302
            LD++  LVEPACGA+L+A+Y+G L ++ AE R      ++VV+VCGG  I    L E+K
Sbjct:  265 LDDERMLVEPACGAALAAIYSGILWRLQAEGRLSSALASVVVIVCGGNNISSQQLQELK 323
[Close]
BLAST of SMED30028170 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000005648.1 (pep scaffold:Pmarinus_7.0:GL478306:28969:31470:-1 gene:ENSPMAG00000005123.1 transcript:ENSPMAT00000005648.1 gene_biotype:protein_coding transcript_biotype:protein_coding)

HSP 1 Score: 50.447 bits (119), Expect = 2.339e-7
Identity = 26/61 (42.62%), Postives = 40/61 (65.57%), Query Frame = 3 
Query:  132 ILDEQNCLVEPACGASLSALYNGTLDQM-AECRECDL--NIVVVVCGGRCIDVTSLIEMKQ 305
             LD++  LVEPACGA+L+A+Y+G + ++ AE R   L   +V VVCGG  + +  L E ++
Sbjct:  158 FLDDERMLVEPACGAALAAVYSGAVRRLVAEGRLGPLPGPVVAVVCGGSGVTLGQLREWRE 218
The following BLAST results are available for this feature:
BLAST of SMED30028170 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 SMED30028170 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 SMED30028170 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 SMED30028170 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 SMED30028170 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 SMED30028170 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Sdsl1.899e-647.46serine dehydratase-like [Source:MGI Symbol;Acc:MGI... [more]
Sdsl1.899e-647.46serine dehydratase-like [Source:MGI Symbol;Acc:MGI... [more]
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BLAST of SMED30028170 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 SMED30028170 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 SMED30028170 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 SMED30028170 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
ENSPMAT00000005648.12.339e-742.62pep scaffold:Pmarinus_7.0:GL478306:28969:31470:-1 ... [more]
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BLAST of SMED30028170 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 SMED30028170 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 SMED30028170 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 SMED30028170 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028170 ID=SMED30028170|Name=SMED30028170|organism=Schmidtea mediterranea sexual|type=transcript|length=1608bp
TAAAAATCCCCCAAATTAAAGAAAGTTATCCCCGTGAGACGTGCCCGCAT
ATTAGGCGTGTGCAAAACGTTTTGACTATCAATTTGTATAGTAATCATCA
TCGAATTGCAGATTCAATAATCTTTTGATTGATTCTAGATGAACAAAACT
GCTTAGTGGAACCGGCTTGTGGCGCATCATTATCAGCTTTATACAACGGC
ACATTGGACCAAATGGCAGAATGCCGCGAGTGCGACCTGAATATAGTCGT
GGTGGTGTGTGGGGGCCGATGTATCGACGTGACGAGTCTCATCGAAATGA
AACAAGTATTTTCCGCAATCAATCCCAACACCGGTCCCTATGACAACGTC
GTCAGTAACTCAGTCTATGACAGTCTCTCGAGTCCCTATGACGCTGCTGC
GGCAGCCGTCGTTGTCAACGATCGATTTCTGTCGATGAATATCAATAATA
ATCAGTCCGATCGATTGGAAACCGCCGACGTATTTTATCCCTCCTCGAAT
CGTTTCGATCCCTCCATTCCGAGCTACAATCACATGTTCCCGTCGCTAAC
GAAAACGACATCAGAGCAACCGTCAAACACCAACACCAATTGCGCACCGA
TTCATCATAAGTCGAATATTCTCACCGAAAATAAGTTTCTCGGTTACCGA
CATCGCAACAGTAACCACCACGGTAACAACGGTAGCAACTACAACTACCA
ATATTCATCATCATCGATCAACACTAGCAATAACAACATCAATAGCAGCA
ATTTAATCAATAACAATCTAATCAATACTAACAATATAATCAATAATGAT
CAAAGTTACATGTCATCCAATGACCTTATGTCATCTCCCGTCGGCAGTCA
GCATTCGGACAAGGAGAACCGAATGTTACCGAATTGATTGTCATTATTAT
TATTGTTGATATATAGTATTGATTGATTTATATAATATCGATTGATTGAT
TTATAATTTCGATTGATTTATATAATATCGATCGTTCGATTTACCCGAGA
GACTCACAGAACAAGAGAACGAAAATAGCTGGCTTAGATTAGTTTTATAA
TTTCTTTATTTTTATTGATTTGATCGATTAAATTTGAATAATAATAATAA
CTACTCATTTTTTAAAGCGAATGTGTAATTTCTATTGATTTGATTGGCTG
ATTGTGACGATGAGATGGATTGCTTTTTGTTTTTCCTATCGCGATTTGTT
GAGTGTTGCGGTTGATTATTATTATTTTTATTACTATTATTATTATTTCT
TTGAGAAGGAACATTGGGGCTTTGTGTGTATAAATATTTGTGTAAACATA
GTTTAATTGCATTTTATTACGGATATTCTTATTATTACATACGGCATTGT
CCTAGGATTGTTTTATTATTTTGCGCCTGCACACAATTAGTCAGCGCTTA
ATTTCTGTATATTACTACTACTACTAATATAGTCTATTAGATTTTTGCTC
ATAATAGATTATTTGACAATTAAAAGATATTTATTTTTTGTAATTCGGTT
CCTATCGGTTAAAATTTGAATTTTTTGCATATTTTCATGGTTGACTTGTC
GAGGTATCTGTATATTTATAGTGTAGTTATTTTACTAAAAATACAATTTT
GCTGTTGG
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protein sequence of SMED30028170-orf-1

>SMED30028170-orf-1 ID=SMED30028170-orf-1|Name=SMED30028170-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=225bp
MAECRECDLNIVVVVCGGRCIDVTSLIEMKQVFSAINPNTGPYDNVVSNS
VYDSLSSPYDAAAAAVVVNDRFLSMNINNNQSDRLETADVFYPSSNRFDP
SIPSYNHMFPSLTKTTSEQPSNTNTNCAPIHHKSNILTENKFLGYRHRNS
NHHGNNGSNYNYQYSSSSINTSNNNINSSNLINNNLINTNNIINNDQSYM
SSNDLMSSPVGSQHSDKENRMLPN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0000463cholinergic neuron
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: molecular function
TermDefinition
GO:0003941L-serine ammonia-lyase activity
GO:0016829lyase activity