SMED30010551

Overview
NameSMED30010551
Smed IDSMED30010551
Length (bp)2538
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 SMED30010551 (SMED30010551) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30010551 (SMED30010551) 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 SMED30010551 (SMED30010551) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010551 (SMED30010551) 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



SMED30010551

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
tail regionSMED30010551 SmedASXL_007236SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
X2 cellSMED30010551 SmedASXL_007236SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30010551SMESG000057219.1 dd_Smed_v4_15701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30010551SMESG000057219.1 dd_Smed_v4_15701_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010551SMESG000030578.1 SMESG000020466.1 Contig32548newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010551SMESG000030578.1 SMESG000020466.1 Contig32548uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30010551 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002863:68560..71202 -9754
v31.011475:4722..7336 +9334
Homology
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BLAST of SMED30010551 vs. Planmine SMEST
Match: SMESG000004514.1 (SMESG000004514.1)

HSP 1 Score: 114.39 bits (285), Expect = 2.077e-29
Identity = 62/138 (44.93%), Postives = 85/138 (61.59%), Query Frame = 1 
Query: 1813 MTKLTPRSPVNERLPSSARPTQG--RWMIKFDDRTAA*GRQLLWDYRYTVATSVPVTWPAQFDSMRGTSLLGLAIKREPGRNPIREARKRIESLVLRLDKENRELQQRRRTAQMGLDRINRDIIVGRVPGSGGYVPDY 2220
            M++LTP+   N R  +  R   G  R +I+F    +A  R +LWDY Y+V+T    T PA+   +    + G+AIKREPGRNP RE R+++E  +L L +E R LQ RRR  Q+ LD+INRDI  GR+  +G Y PDY
Sbjct:    2 MSELTPQLSTNGRQSTVRRHVPGPEREIIQFSSTASAQCRHILWDYEYSVSTPGDSTLPARPGLIEDLDIPGIAIKREPGRNPARETRQKVEFYLLLLVEEERRLQHRRRMPQVELDKINRDIAAGRILCTGVYAPDY 139
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BLAST of SMED30010551 vs. Planmine SMEST
Match: SMESG000074058.1 (SMESG000074058.1)

HSP 1 Score: 106.686 bits (265), Expect = 5.063e-27
Identity = 57/119 (47.90%), Postives = 78/119 (65.55%), Query Frame = 1 
Query: 1891 IKFDDRTAA*GRQLLWDYRYTVAT-SVPVTWPAQFDSMRGTSLLGLAIKREPGRNPIREARKRIESLVLRLDKENRELQQRRRTAQMGLDRINRDIIVGRVPGSGGYVPDYEVSFDLND 2244
            ++FD  TAA  RQ+LWDYRY V T S P+       S++  ++  + IKR+PGRNP REAR+R+E  + RL+K NR+LQ RRR AQ  L RIN +I  G +     Y P+Y VS+++ND
Sbjct:    1 MQFDSNTAAQCRQILWDYRYMVTTRSDPL------GSLKEMNIHSITIKRKPGRNPAREARQRVEYYLFRLEK-NRQLQHRRRMAQRELCRINFEIAAGIILCLDTYAPEYNVSYEIND 112
[Close]
BLAST of SMED30010551 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1)

HSP 1 Score: 98.2117 bits (243), Expect = 5.560e-23
Identity = 56/161 (34.78%), Postives = 92/161 (57.14%), Query Frame = 1 
Query: 1843 NERLPSSARPTQGRWMIKFDDRTAA*GRQLLWDYRYTVATSVPVTWP--AQFDSMRGTSLLGLAIKREPGRNPIREARKRIESLVLRLDKENRELQQRRRTAQMGLDRINRDIIVGRVPGSGGYVPDYEVSFDLNDLTLRIIAALTQVMIPE*LTHRTC*N 2319
            N R P  +     R  ++    +AA  RQ+LWD  Y ++T    +WP  +++ +     L  +AIKREPG NP REAR+R E   +++++  R+  ++   A+  L ++NRDI  G +P + G+ P+Y VSF+L+D  L  + A T++++PE L   T  N
Sbjct:   28 NRRDPHGSWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSKYQAEE-IELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRN 187
[Close]
BLAST of SMED30010551 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 98.5969 bits (244), Expect = 1.901e-22
Identity = 68/218 (31.19%), Postives = 109/218 (50.00%), Query Frame = 1 
Query: 1678 MKMFYNIIMSAQM---NIQHQHRRPEKRSREQTNRTAQEKEFREPNLRMTKLTPRSPVNERLPSSARPTQGRWMIKFDDRTAA*GRQLLWDYRYTVATSVPVTWPAQFD-SMRGTSLLGLAIKREPGRNPIREARKRIESLVLRLDKENRELQQRRRTAQMGLDRINRDIIVGRVPGSGGYVPDYEVSFDLNDLTLRIIAALTQVMIPE*LTHRTC*N 2319
            MK   NI++   +    I+H+ RR E   + Q     +  ++R                 R P  +     R  ++    +AA  RQ+LWD  Y ++T    +WP + +       L  +AIKREPG NP REAR+R E   ++ ++  R+ Q++   A+  L ++NRDI  G +P + G+ P+Y VSF+L+D  L  + A T+++IPE L   T  N
Sbjct:   40 MKAPTNIVLPVNLFNGPIRHRDRRDEHSYQCQHPTKKERNQYR-----------------RDPHGSWSDNSRVTLQIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRN 240
[Close]
BLAST of SMED30010551 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1)

HSP 1 Score: 103.219 bits (256), Expect = 4.998e-22
Identity = 55/158 (34.81%), Postives = 90/158 (56.96%), Query Frame = 1 
Query: 1849 RLPSSARPTQGRWMIKFDDRTAA*GRQLLWDYRYTVATSVPVTWPAQFD-SMRGTSLLGLAIKREPGRNPIREARKRIESLVLRLDKENRELQQRRRTAQMGLDRINRDIIVGRVPGSGGYVPDYEVSFDLNDLTLRIIAALTQVMIPE*LTHRTC*N 2319
            R P  +     R  ++    +AA  RQ+LWD  Y ++T    +WP + +       L  +AIKREPG NP REAR+R +   +++++  R+  ++  +A+  L ++NRDI  G +P + G+ P+Y VSF+L+D  L  + A T+++IPE L   T  N
Sbjct: 1640 RDPHGSWSDNSRVTLEIPSASAARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTLRN 1797
The following BLAST results are available for this feature:
BLAST of SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 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 SMED30010551 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000004514.12.077e-2944.93SMESG000004514.1[more]
SMESG000074058.15.063e-2747.90SMESG000074058.1[more]
SMESG000027782.15.560e-2334.78SMESG000027782.1[more]
SMESG000004883.11.901e-2231.19SMESG000004883.1[more]
SMESG000057533.14.998e-2234.81SMESG000057533.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010551 ID=SMED30010551|Name=SMED30010551|organism=Schmidtea mediterranea sexual|type=transcript|length=2538bp
AGATCAACCTCCAAATAAGCAAACTTACAACATTAATAGTTCTTATCAAG
ACAACCAACCTGATTACCATGGCGATCCTGATTACGCTGATTACCTGAAA
AGCTTACAGTATGAAGAAGAATACTCTGATGGTGATTACTGATGTCGTTT
CTTTTGTTTAATTTCTTACTAGCTGTATAATGTGCTTTTATATTTTTACA
AAGATGCAGAATACTTTGCTGATGATTAATTTTGTTGTTTTGTTGTTTCT
ATGTTGTGGTTTTTATTATAATGTATAAATTTTTACATGTGTCGTAATTA
TGGTTACCTTTGTTTTTTCTGTTGTACTGTACTGCTGTCTTTAATAACTT
TAGAAAGAAAACAAAAACAACCCATACAAATTAAAAGAGATATATTAATA
TATTCACAATGTCGAGATGAATACTGCGAGAGCGCTGATGAGTGTCGCTG
GAATACTTGAGACGGTGATGGAGAGGACTGTGCTTGCCTGGTTATCTCAA
CCGGACAGATGAGGAGAATTGAAGAATGAAATCCTAAAAGAAACTTGATT
GAGTCTGATCTACTGATGGTTGGGCTAGTCCCCTTAAAAGGACACACAGA
CTCTTCAGAGTCTGTTTTCATGAAATAAAATTTATTTAAATTGAGCATAC
GCATAGACCAAGTTAATAATACAAATAGTTCCGATTTTATCCTTGATCGT
GCTATCCGCGGGGGAAGAATGAAGTTTCTGAGATTAACGATGTAATGAAA
TTTGGAAGCACTGCAAAGGATCTTTACTCACTCCGTTTCGATCGTGTAAC
TTCATATCCTCCAGATTGTAATAACCCATGTTACCGATCGATACTAACGC
ACGTCCGAAGAAAATACCGAAAGTTTATGAATTGGTAGCTCCGTTTGTTG
AATGAATTAAAATGAAGAACATAGGGAAGCCGGGTAAAATCACGTAGTAA
ATCCGAGGTAAAATCACAACCTGAAAGACATGAATGAATTATACCCGCTG
AAAATAGTTGATGGCGTAGTAACTGGATAGTAAGTAGACAGTTGTTTGAA
CACCCACGTTAATTGATGAGGCGAATCGTCGGTGCATTACGGCGTAGTAG
ATTGCATCTAGTATACTAATGTAAGCAAAAATGAATGAAATAAGATTACT
TAACCGGTCATTCAATAGCGATGGTGAAAGAGATTGATGCGGTCGCTGGT
AAAGCATAATGATAAAACAATAAGGCCACCTAAAAAGGTAATAACAGTAA
TAAATAATACAAAAATTCTGTTTTGCTTAGTATAAATATTTAATGAGGGC
AATAATCATAAAACAAATACTTAAAAATTTACAATAACTAATGAGCAAAT
AATAATGATACTAACATTAAGAATAAGAATAACAGTAGTAATTTTAACAG
TAATAACAATTATAGTAGTACCATGGCAATAAGGAAAAATCGTCACAAGC
CCCTCAGATAACCGTACTAACCATAATGTCAATAATAACAATAGGGACAT
TTATAAAACTTATGGATAATACAGCCCACTAAATAAGACCAATGCAGCTA
AAATCAAACATACAGTATTATTAATACATGGAATATAATGCTTCAAATGC
ACGTAATAACAAGGTATTGTATTACGTGTCGGTACAGTTGAGATTAGTGA
CATGACCAATAATGGTATATAAGAAGCATGAAAATGTTCTACAATATCAT
TATGTCAGCTCAGATGAACATTCAGCATCAACATAGGAGACCGGAAAAAC
GTTCTCGAGAACAGACTAACCGAACGGCTCAGGAGAAGGAGTTCAGAGAA
CCAAATCTCAGGATGACCAAACTAACTCCCCGATCACCAGTCAACGAAAG
ACTACCTTCTTCAGCAAGACCGACGCAGGGACGTTGGATGATTAAATTCG
ATGACAGGACGGCAGCGTAAGGACGCCAGCTTCTGTGGGATTATAGGTAC
ACCGTCGCAACATCTGTACCAGTCACTTGGCCAGCTCAATTCGACTCAAT
GAGAGGTACGAGTCTCCTTGGACTCGCTATTAAAAGGGAACCTGGACGGA
ACCCTATCCGAGAAGCTCGCAAGAGGATAGAGTCGCTAGTTCTTCGCTTG
GATAAAGAGAATCGGGAACTACAGCAACGACGTCGGACGGCCCAAATGGG
GCTGGACAGGATAAATCGAGATATAATCGTCGGGAGAGTTCCAGGCTCGG
GCGGATATGTGCCGGATTACGAGGTCTCCTTCGATCTCAACGATCTGACC
TTGAGAATTATAGCCGCTTTAACGCAGGTGATGATCCCGGAGTAGTTGAC
TCACCGGACATGCTGAAATGACTGGATACGCTGCAAGAAGGAAGACACTT
GCATGAAAGAAAGTGTCGTAGGTCAAGATCTCGACCTAACAATTCTTCTT
GGAGAAATTTTGTGAATGGCAATTATTATAAATCATAAATAATGTGTTGT
TTTTCCTTTTTATAATTCGTATTATTGACTTATTTTAATAACAAACTTGA
ATGATTAAAGTTACATTACCCAATCTAGAGTTAAAGCC
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protein sequence of SMED30010551-orf-1

>SMED30010551-orf-1 ID=SMED30010551-orf-1|Name=SMED30010551-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=117bp
MRMLNLNKFYFMKTDSEESVCPFKGTSPTISRSDSIKFLLGFHSSILLIC
PVEITRQAQSSPSPSQVFQRHSSALSQYSSRHCEYINISLLICMGCFCFL
SKVIKDSSTVQQKKQR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000421tail
PLANA:0002111X2 cell