SMED30024056

Overview
NameSMED30024056
Smed IDSMED30024056
Length (bp)1064
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 SMED30024056 (SMED30024056) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30024056 (SMED30024056) 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 SMED30024056 (SMED30024056) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30024056 (SMED30024056) 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




SMED30024056

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
head regionSMED30024056 SmedASXL_013456SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
epidermisSMED30024056 dd_Smed_v4_14719_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30024056 dd_Smed_v4_14719_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 3 cellSMED30024056 dd_Smed_v4_14719_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
SMED30024056 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000248:151523..152586 +5320
v31.002146:730..1787 -3939
v31.019676:4703..5760 -3921
Homology
BLAST of SMED30024056 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1)

HSP 1 Score: 99.7525 bits (247), Expect = 6.151e-36
Identity = 50/78 (64.10%), Postives = 59/78 (75.64%), Query Frame = 1
Query:  541 SPDLAAQYRLSLWDANYSLSTLGYNSWPIRESSRQDEIEISSLAIKREPS*NRPDKRDSAQNISLYRLEALVRKFQWR 774
            +PD+AAQYR SLWD +YSL+TLG NSWPIR+ SR +EIE+ SLAIKREP  N   +       SLYRLE LVRKFQW+
Sbjct:   16 TPDMAAQYRQSLWDVSYSLATLGDNSWPIRDKSRDNEIELLSLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWK 93          

HSP 2 Score: 70.0922 bits (170), Expect = 6.151e-36
Identity = 34/62 (54.84%), Postives = 42/62 (67.74%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVLPVNLFNGPKRHR 947
            ++   L+ INA IA+GEIPSTDGYA DYG+   L DP LT+M   TN +LP  LFN   RH+
Sbjct:   96 MTQRHLKQINATIATGEIPSTDGYAQDYGLLFELNDPVLTQMH--TNAILPAQLFNERIRHQ 155          
BLAST of SMED30024056 vs. Planmine SMEST
Match: SMESG000058576.1 (SMESG000058576.1)

HSP 1 Score: 96.2857 bits (238), Expect = 2.694e-28
Identity = 44/64 (68.75%), Postives = 53/64 (82.81%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVLPVNLFNGPKRHRDR 953
            ++  RLE INAAIASGEI STDGYAPDYG+S  L++P+LTRM+A TNI+LP  LFNG  RHR+R
Sbjct:  202 MARRRLEQINAAIASGEILSTDGYAPDYGISFELKNPALTRMQALTNIILPAKLFNGSMRHRNR 265          

HSP 2 Score: 48.1358 bits (113), Expect = 2.694e-28
Identity = 25/51 (49.02%), Postives = 31/51 (60.78%), Query Frame = 1
Query:  622 PIRESSRQDEIEISSLAIKREPS*NRPDKRDSAQNISLYRLEALVRKFQWR 774
            P +E  RQDEIEI S+AI  +   N  ++       SLYRLE LV KFQW+
Sbjct:  149 PSQEDPRQDEIEIPSIAINHKLGRNPAEEARQHAEFSLYRLEELVLKFQWK 199          
BLAST of SMED30024056 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1)

HSP 1 Score: 107.071 bits (266), Expect = 1.178e-26
Identity = 57/98 (58.16%), Postives = 66/98 (67.35%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVLPVNLFNGPKRHRDR--EMTTPISAIIQQRRNGSNA*SHSKTEDSEDLT 1049
            ++  RLE INA IASGEIPSTDGYAPDYGVS  LRDP+  RM+APTNIVLPVNLFNGP RHRDR  E +       ++ RN      H    D+  +T
Sbjct:    1 MARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDPA--RMKAPTNIVLPVNLFNGPIRHRDRRDEHSYQCQHPTKKERNQYRRDPHGSWSDNSRVT 96          

HSP 2 Score: 67.3958 bits (163), Expect = 3.295e-22
Identity = 32/62 (51.61%), Postives = 42/62 (67.74%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVLPVNLFNGPKRHR 947
            ++ +RL  +N  IASG IPSTDG+ P+YGVS  L DP LT+M APT +V+P  L     R+R
Sbjct:  180 LARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNR 241          

HSP 3 Score: 56.225 bits (134), Expect = 3.295e-22
Identity = 31/72 (43.06%), Postives = 42/72 (58.33%), Query Frame = 1
Query:  553 AAQYRLSLWDANYSLSTLGYNSWPIRESSRQDEIEISSLAIKREPS*NRPDKRDSAQNISLYRLEALVRKFQ 768
            AA+YR  LWD  Y LST G +SWP R   + +E+E+ S+AIKREP  N   +       +  + E L RK+Q
Sbjct:  104 AARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEVELPSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQ 175          
BLAST of SMED30024056 vs. Planmine SMEST
Match: SMESG000003895.1 (SMESG000003895.1)

HSP 1 Score: 74.3294 bits (181), Expect = 2.056e-24
Identity = 37/75 (49.33%), Postives = 48/75 (64.00%), Query Frame = 1
Query:  550 LAAQYRLSLWDANYSLSTLGYNSWPIRESSRQDEIEISSLAIKREPS*NRPDKRDSAQNISLYRLEALVRKFQWR 774
             AA+YR +LWD  YSL+T G + WP R  SR +E E+ S+AIKREP  N   +       +LYRLE L +KF+WR
Sbjct:  152 FAARYRQALWDRQYSLATCGNDEWPCRSISRDNETELPSVAIKREPGRNPSRQIRQKAKFTLYRLENLKKKFRWR 226          

HSP 2 Score: 56.9954 bits (136), Expect = 2.056e-24
Identity = 27/50 (54.00%), Postives = 36/50 (72.00%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVL 911
            ++  +L  INA IASG   STDG+APDYGVS  L DP+L ++  PT++VL
Sbjct:  229 MARRKLARINADIASGLKLSTDGFAPDYGVSFDLHDPALPKIETPTHLVL 278          
BLAST of SMED30024056 vs. Planmine SMEST
Match: SMESG000026563.1 (SMESG000026563.1)

HSP 1 Score: 70.4774 bits (171), Expect = 2.832e-23
Identity = 33/62 (53.23%), Postives = 43/62 (69.35%), Query Frame = 3
Query:  762 ISMERLEMINAAIASGEIPSTDGYAPDYGVSIGLRDPSLTRMRAPTNIVLPVNLFNGPKRHR 947
            ++ +RL  +N  IASG IPSTDG+ P+YGVS  L DP LT+M APT +V+P NL     R+R
Sbjct:  717 LARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPENLVQSTLRNR 778          

HSP 2 Score: 56.9954 bits (136), Expect = 2.832e-23
Identity = 31/72 (43.06%), Postives = 42/72 (58.33%), Query Frame = 1
Query:  553 AAQYRLSLWDANYSLSTLGYNSWPIRESSRQDEIEISSLAIKREPS*NRPDKRDSAQNISLYRLEALVRKFQ 768
            AA+YR  LWD  Y LST G +SWP R   + +EIE+ S+AIKREP  N   +       +  ++E L RK+ 
Sbjct:  641 AARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYH 712          
The following BLAST results are available for this feature:
BLAST of SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 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 SMED30024056 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000026733.16.151e-3664.10SMESG000026733.1[more]
SMESG000058576.12.694e-2868.75SMESG000058576.1[more]
SMESG000004883.11.178e-2658.16SMESG000004883.1[more]
SMESG000003895.12.056e-2449.33SMESG000003895.1[more]
SMESG000026563.12.832e-2353.23SMESG000026563.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024056 ID=SMED30024056|Name=SMED30024056|organism=Schmidtea mediterranea sexual|type=transcript|length=1064bp
CCAGAGTGAAACAGTCCTCCGCACCAACTGTTACGCCTTGATAATATAAA
TAAAGCGACTCTAATGACTAGCCATTATAAATCTGAGATCATGAAGACAT
CGAACATCAAGAAGACTACGCCAATGGGACAAACGAGAGGTCGACCACTG
AGAGCAGATAAAACAATCGACTGGGACCCTCCACGACTTTCCGACCACTA
GTAGGATAATACCACGATCTTCCCCGAAGAAAGCAAGGGTCTATTAATTT
ATTCAATTTACGTAAAATATCCATCTACTGAGTGTACAAATGAACCGCAG
TGTTAATTACTAAAGCCAGATGCAAATATCACAAATGCAGTGGAAAAGAT
GTAACTGACTCGCATGTGTCAAGAAGGTTTGCGACTCCAGAACGCGTTGA
CATACAATTATTATAATAATATTGCTGGATAAAGAAAATATAATTTGGAA
CCAAAAATTACCTTTATTTTATTTTCCAGCGGATGATCGACCAACAGGGA
CCGAAATCTGGAGCGACGAAGACAAGGTGGCCATTCGAGTAGCCCCGACC
TGGCAGCACAATACAGATTATCATTATGGGACGCCAACTACAGCCTCTCC
ACATTGGGATATAATAGTTGGCCCATCAGAGAAAGCTCCAGACAAGATGA
GATCGAGATATCCAGTCTCGCCATCAAGCGCGAGCCAAGTTGAAACCGGC
CTGATAAGCGCGACAGCGCGCAGAATATTTCACTCTATCGATTGGAAGCA
CTGGTACGGAAATTTCAATGGAGAGATTGGAAATGATCAACGCCGCGATT
GCCTCAGGTGAGATTCCCAGCACGGATGGATATGCGCCAGACTATGGCGT
CTCAATTGGGTTAAGAGATCCATCACTCACACGGATGCGAGCACCCACAA
ATATCGTCCTTCCGGTCAACCTATTCAATGGCCCAAAACGACACCGGGAC
AGAGAGATGACCACTCCTATCAGTGCCATCATCCAACAAAGAAGGAACGG
AAGCAATGCATGAAGCCACTCCAAGACCGAAGATTCGGAAGACCTTACTG
ATAATGAGATCACG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0000418head