SMED30010912

Overview
NameSMED30010912
Smed IDSMED30010912
Length (bp)399
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 SMED30010912 (SMED30010912) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010912 (SMED30010912) 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 SMED30010912 (SMED30010912) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010912 (SMED30010912) 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




SMED30010912

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30010912h1SMcG0022001 SmedASXL_015728SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30010912h1SMcG0022001 dd_Smed_v4_11259_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30010912h1SMcG0022001 dd_Smed_v6_11259_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30010912h1SMcG0022001 dd_Smed_v4_11259_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
SMED30010912 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002605:22027..24655 +1879
Homology
BLAST of SMED30010912 vs. Ensembl Nematostella
Match: EDO30135 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T1N0])

HSP 1 Score: 43.1282 bits (100), Expect = 9.712e-6
Identity = 21/76 (27.63%), Postives = 35/76 (46.05%), Query Frame = -1
Query:   76 FGEETKNFIKKNFQTRTCYKYKEKRKDF--CSCNRELIEHKDKS----NDPENWSYSNNTMLNPCTKFGLINFNGY 285
              +  K++I +NF  R C ++  K  D   C C R    H  ++       E W+ ++ T  +P   +G I+F GY
Sbjct:   28 LSQSKKSWIARNFSRRECIRFVPKSHDVSRCKCGRPRERHSQQALESGQGSEEWNVASCTTKHPTNAYGEIDFEGY 103          
BLAST of SMED30010912 vs. Planmine SMEST
Match: SMESG000005057.1 (SMESG000005057.1)

HSP 1 Score: 245.743 bits (626), Expect = 2.571e-78
Identity = 113/114 (99.12%), Postives = 113/114 (99.12%), Query Frame = -1
Query:    1 MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 342
            MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEH DKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR
Sbjct:    1 MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHTDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 114          
BLAST of SMED30010912 vs. Planmine SMEST
Match: SMESG000005057.1 (SMESG000005057.1)

HSP 1 Score: 245.743 bits (626), Expect = 1.853e-76
Identity = 113/114 (99.12%), Postives = 113/114 (99.12%), Query Frame = -1
Query:    1 MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 342
            MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEH DKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR
Sbjct:    1 MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHTDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 114          
BLAST of SMED30010912 vs. Planmine SMEST
Match: SMESG000005061.1 (SMESG000005061.1)

HSP 1 Score: 145.976 bits (367), Expect = 4.818e-43
Identity = 70/114 (61.40%), Postives = 80/114 (70.18%), Query Frame = -1
Query:    1 MEMENPKHSSKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 342
            MEM+N    +K E     GF ++ + FI K F TRTCYKYKEK KD C CNR L  H +KSN PE WSYSNNT L+ C KFG I F+GY ++P EH PKFIRFDC EDCDATCR
Sbjct:    1 MEMKN----TKSEITIKNGFEDQIQEFINKKFNTRTCYKYKEKSKDICHCNRHLNHHTNKSNSPEEWSYSNNTTLDSCVKFGRIKFSGYPNLPHEHWPKFIRFDCEEDCDATCR 110          
BLAST of SMED30010912 vs. Planmine SMEST
Match: SMESG000005061.1 (SMESG000005061.1)

HSP 1 Score: 143.665 bits (361), Expect = 4.303e-42
Identity = 66/105 (62.86%), Postives = 75/105 (71.43%), Query Frame = -1
Query:    1 SKLEFETIKGFGEETKNFIKKNFQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDCAEDCDATCR 315
            +K E     GF ++ + FI K F TRTCYKYKEK KD C CNR L  H +KSN PE WSYSNNT L+ C KFG I F+GY ++P EH PKFIRFDC EDCDATCR
Sbjct:    4 TKSEITIKNGFEDQIQEFINKKFNTRTCYKYKEKSKDICHCNRHLNHHTNKSNSPEEWSYSNNTTLDSCVKFGRIKFSGYPNLPHEHWPKFIRFDCEEDCDATCR 108          
BLAST of SMED30010912 vs. Planmine SMEST
Match: SMESG000004977.1 (SMESG000004977.1)

HSP 1 Score: 78.9518 bits (193), Expect = 5.688e-18
Identity = 39/79 (49.37%), Postives = 46/79 (58.23%), Query Frame = -1
Query:   28 FIKKNFQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKFGLINFNGYDDIPREHLPKFIRFDC 264
            FIKK FQ R CYKYK +  + C C     +H+D     E WS  NNT    C  FG+INF GY+DI   H P FIRF+C
Sbjct:    4 FIKKYFQIRYCYKYKGEIFETCKCGNIKTDHQDFPIKDEIWSLENNTKCRTCDTFGIINFTGYNDIITNHYPHFIRFNC 82          
The following BLAST results are available for this feature:
BLAST of SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 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 SMED30010912 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO301359.712e-627.63Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30010912 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 SMED30010912 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005057.12.571e-7899.12SMESG000005057.1[more]
SMESG000005057.11.853e-7699.12SMESG000005057.1[more]
SMESG000005061.14.818e-4361.40SMESG000005061.1[more]
SMESG000005061.14.303e-4262.86SMESG000005061.1[more]
SMESG000004977.15.688e-1849.37SMESG000004977.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010912 ID=SMED30010912|Name=SMED30010912|organism=Schmidtea mediterranea sexual|type=transcript|length=399bp
CCTGCAAGTTGCATCGCAATCTTCTGCGCAATCAAATCTGATAAATTTGG
GAAGATGTTCCCGAGGAATGTCGTCGTATCCGTTGAAATTGATCAATCCA
AACTTTGTGCATGGATTAAGCATTGTGTTGTTTGAATAAGACCAATTTTC
TGGATCGTTTGATTTGTCTTTGTGTTCAATCAGTTCCCGATTGCATGAGC
AGAAATCCTTTCTTTTCTCTTTATATTTGTAACATGTTCTTGTTTGAAAA
TTTTTCTTAATAAAGTTTTTTGTTTCTTCTCCAAATCCCTTTATGGTTTC
GAATTCAAGTTTGGAGGAATGCTTAGGATTTTCCATTTCCATTGCGAATG
TATCATTAAAATTTTCAATCCCAACTAAAATTTCAACTTTTGATTTCCA
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protein sequence of SMED30010912-orf-1

>SMED30010912-orf-1 ID=SMED30010912-orf-1|Name=SMED30010912-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=133bp
WKSKVEILVGIENFNDTFAMEMENPKHSSKLEFETIKGFGEETKNFIKKN
FQTRTCYKYKEKRKDFCSCNRELIEHKDKSNDPENWSYSNNTMLNPCTKF
GLINFNGYDDIPREHLPKFIRFDCAEDCDATCR
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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
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell