SMED30014534

Overview
NameSMED30014534
Smed IDSMED30014534
Length (bp)1616
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 SMED30014534 (SMED30014534) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014534 (SMED30014534) 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 SMED30014534 (SMED30014534) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014534 (SMED30014534) 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



SMED30014534

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 SmedASXL_013116SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v4_14062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v4_14062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v4_14062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v4_14062_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v6_14062_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30014534SMESG000047985.1 SMESG000035720.1 SMESG000035719.1 dd_Smed_v4_14062_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
Alignments
SMED30014534 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004140:11566..34814 +7786
Homology
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BLAST of SMED30014534 vs. Planmine SMEST
Match: SMESG000047985.1 (SMESG000047985.1)

HSP 1 Score: 323.168 bits (827), Expect = 1.984e-109
Identity = 158/159 (99.37%), Postives = 158/159 (99.37%), Query Frame = 3 
Query: 1065 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK 1541
            MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQ PYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK
Sbjct:    1 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQRPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK 159
[Close]
BLAST of SMED30014534 vs. Planmine SMEST
Match: SMESG000047985.1 (SMESG000047985.1)

HSP 1 Score: 320.472 bits (820), Expect = 2.200e-108
Identity = 157/158 (99.37%), Postives = 157/158 (99.37%), Query Frame = 3 
Query: 1068 MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK 1541
            MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQ PYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK
Sbjct:    1 MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQRPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIHSNSVIDWDQISEMIKSPTLK 158
[Close]
BLAST of SMED30014534 vs. Planmine SMEST
Match: SMESG000035720.1 (SMESG000035720.1)

HSP 1 Score: 273.478 bits (698), Expect = 3.701e-90
Identity = 133/134 (99.25%), Postives = 133/134 (99.25%), Query Frame = 3 
Query: 1065 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQ 1466
            MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQ PYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQ
Sbjct:    1 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQRPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQ 134
[Close]
BLAST of SMED30014534 vs. Planmine SMEST
Match: SMESG000035720.1 (SMESG000035720.1)

HSP 1 Score: 263.077 bits (671), Expect = 4.596e-86
Identity = 127/129 (98.45%), Postives = 127/129 (98.45%), Query Frame = 3 
Query: 1065 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNT 1451
            MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQ PYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYN 
Sbjct:    1 MMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQRPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNV 129
[Close]
BLAST of SMED30014534 vs. Planmine SMEST
Match: SMESG000035720.1 (SMESG000035720.1)

HSP 1 Score: 259.996 bits (663), Expect = 5.350e-85
Identity = 126/128 (98.44%), Postives = 126/128 (98.44%), Query Frame = 3 
Query: 1068 MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNT 1451
            MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQ PYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYN 
Sbjct:    1 MLYALKNSQHQTLLKSSYLQSESILKCYKKTLQRPYFEKVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNLENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNV 128
The following BLAST results are available for this feature:
BLAST of SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 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 SMED30014534 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000047985.11.984e-10999.37SMESG000047985.1[more]
SMESG000047985.12.200e-10899.37SMESG000047985.1[more]
SMESG000035720.13.701e-9099.25SMESG000035720.1[more]
SMESG000035720.14.596e-8698.45SMESG000035720.1[more]
SMESG000035720.15.350e-8598.44SMESG000035720.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014534 ID=SMED30014534|Name=SMED30014534|organism=Schmidtea mediterranea sexual|type=transcript|length=1616bp
GAGAGAAAAATTACCTCAGACAGGGGATAAAACTCCAAGTTAAGTAAAAG
TTTTTATATCTATTCTAACAATTAATTTAAGGTTATAAAACGGATATTTT
CAAGCAAATCGATAAAAATCTTGCGAAAGAAAAGAATTTTAATCAAATTA
CAGATTATGATAACATTAGTAACATTGAATACAATGATTATGGGTTAATA
AATCAAGCTAAAAGAGATCATGATGGGGAAAATAAAAAGCTTACTGCAGA
TTTGCGTATAATACCAATATTACCACCAGATATGCTTGGACAAGTACATT
TTCAAACAGGAAACAATGCCAAGCATTTCTTAGCGATAAAAAGTATCGAT
GAAAATGGATGGAATGAGCTATTAGACATTAATATGAGTGATAAAAATGA
TGTATATAGTTCAGAAAATATTAGTAATTTTTACAATGACGAAAGTTTGT
TAAATATACATAAAACGGCGAATTTTCATCAAACTTTAAATAAAACCTTT
GGTAACATGGATAAGAAAATATCAGAAATTCAAAAAAATCCTTCCGACTT
AAAAGAAGAATCCACAATTAATACTATGAGTTATTTGAATTCAAACAAAA
ATCATTGTTTTGAAAATAAAAGCGACAAATCAATAAATGACCGGTTCGAG
AATTCAAAGGTACTTGCTGTCAAATACGAAGAAACCAGCAGTTCCAAATC
AGATGTTTTATTATTTTCTGATCCCTCTTTATCTTTAAGTGGTACCGATG
TTTCGAATATATCTTCTCGAAGTTTGTCCAAAATGCAATTCATGCCAAAA
TTAAATCTTGATAATATTGGTACCAACAAAACTGAAAATACAGAATTTTC
TAACCATAATGAAAAAACTCTCGATAAAATATCTATCAAACCTCGTTCTC
TGATTAATAAAACAAGATCTCGAAATTATATCGACAAATCGAATTACTTC
CGTAGAAAATATGACGGGAAACAATTAGCTTTGAAGGTTTTAAATCAGAT
TGGTTTACCTTTGTCGTCTTCAGAAATTCCTATAAAAACTATAAATAGTG
TAACTTCTAACGAAATGATGCTTTATGCTCTGAAAAATAGTCAGCATCAA
ACTTTACTTAAATCGAGTTACTTACAATCTGAAAGTATCTTAAAATGTTA
CAAGAAAACTTTACAGAGTCCATATTTTGAAAAAGTTCGACTTCAGCGGC
CTGAAATAACTCGTCGCGAAATCTCTAGGCCCTTTGCTTATTCGAGTAGT
TTAGCAACTTTACATCCAAAAATAACTAGTTTTAAGGATTTAAAAAATAC
GAAAAATGTATTTTTGGAAACGTTGAATTTGGAAAATGAAATATCTCAAG
GTACTGATATTGAGAGTGTTTTTAGTGACTGGTCAGTTCCACAAAAGGTC
AATGAAATTTTAAAAGATAAATCAAAAAATGATAAAATTGGATATAATAC
CGAAGAATTAAGTCAAATCATATCAATTCATAGCAATAGTGTTATCGATT
GGGATCAAATATCAGAAATGATAAAATCACCTACTTTGAAATAAATATTT
TATTTTCTTTTGGAATTTTGAAATATTGAAATTTTTCATTGTAAACTATT
ACAATTAAGTAATCGG
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protein sequence of SMED30014534-orf-1

>SMED30014534-orf-1 ID=SMED30014534-orf-1|Name=SMED30014534-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=421bp
MLGQVHFQTGNNAKHFLAIKSIDENGWNELLDINMSDKNDVYSSENISNF
YNDESLLNIHKTANFHQTLNKTFGNMDKKISEIQKNPSDLKEESTINTMS
YLNSNKNHCFENKSDKSINDRFENSKVLAVKYEETSSSKSDVLLFSDPSL
SLSGTDVSNISSRSLSKMQFMPKLNLDNIGTNKTENTEFSNHNEKTLDKI
SIKPRSLINKTRSRNYIDKSNYFRRKYDGKQLALKVLNQIGLPLSSSEIP
IKTINSVTSNEMMLYALKNSQHQTLLKSSYLQSESILKCYKKTLQSPYFE
KVRLQRPEITRREISRPFAYSSSLATLHPKITSFKDLKNTKNVFLETLNL
ENEISQGTDIESVFSDWSVPQKVNEILKDKSKNDKIGYNTEELSQIISIH
SNSVIDWDQISEMIKSPTLK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head