SMED30021957

Overview
NameSMED30021957
Smed IDSMED30021957
Length (bp)976
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 SMED30021957 (SMED30021957) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30021957 (SMED30021957) in cells (dots) of each of the 12 neoblast clusters.

 

back to top


 

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 SMED30021957 (SMED30021957) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30021957 (SMED30021957) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top


 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30021957

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30021957SMESG000039476.1 dd_Smed_v4_9685_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30021957SMESG000039476.1 dd_Smed_v4_9685_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30021957SMESG000039476.1 dd_Smed_v4_9685_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
SMED30021957 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006954:9380..10351 +4785
Homology
BLAST of SMED30021957 vs. TrEMBL
Match: gnl|BL_ORD_ID|20337101 (tr|A0A1S6KMK3|A0A1S6KMK3_SCHMD Uncharacterized protein OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 153.68 bits (387), Expect = 1.640e-41
Identity = 89/229 (38.86%), Postives = 128/229 (55.90%), Query Frame = 1
Query:  208 QKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQNLISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFP-----------YFSNPGDSFSAESSEMKKYETN--GMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPV 855
            Q QLGKV +      DE VH  +R L+N +         +H KVLIPGD++NLI Q++I  +M S          +I+C+QLGSNLCWRCSRK+V+ +LK +I   L N +P++  RLIC+ENVLK+MNLPLFS+SE   W +   +S     S+ PLFFP             SN   + ++   E KK+       R +  N +  + + EK     +S++++ PPV
Sbjct:    4 QNQLGKVRVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLIPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSET--FSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEFNYRMINSNKTIQDSKREK-----KSMKYVEPPV 225          
BLAST of SMED30021957 vs. Planmine SMEST
Match: SMESG000039476.1 (SMESG000039476.1)

HSP 1 Score: 463.381 bits (1191), Expect = 9.416e-167
Identity = 224/225 (99.56%), Postives = 225/225 (100.00%), Query Frame = 1
Query:  190 MKLKPFQKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQNLISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFPYFSNPGDSFSAESSEMKKYETNGMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPVIMK 864
            MKLKPFQKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQ+LISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFPYFSNPGDSFSAESSEMKKYETNGMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPVIMK
Sbjct:    1 MKLKPFQKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQSLISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFPYFSNPGDSFSAESSEMKKYETNGMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPVIMK 225          
BLAST of SMED30021957 vs. Planmine SMEST
Match: SMESG000039479.1 (SMESG000039479.1)

HSP 1 Score: 148.673 bits (374), Expect = 3.676e-43
Identity = 85/227 (37.44%), Postives = 128/227 (56.39%), Query Frame = 1
Query:  208 QKQLGKVNLDYNISNDESVHSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQNLISQYRISDRMLSNADSSMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLICVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFP-----------YFSNPGDSFSAESSEMKKYETNGMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPV 855
            Q QLGKV +      DE VH  +R L+N +         +H KVL PGD++NLI Q++I  +M S          +I+C+QLGSNLCWRCSRK+V+ +LK +I   L N +P++  RLIC+ENVLK+MNLPLFS+SE   W +   +S     S+ PLFFP             SN   + ++   E KK+    + +   N++   ++ ++     +S++++ PPV
Sbjct:    4 QNQLGKVKVSQIALKDEIVHKSMRTLINQSGTRPKVYPFIHNKVLNPGDYRNLIEQFQIPTKMHSTIGIQEELPTHIFCHQLGSNLCWRCSRKMVNRKLKEQIETDLTNSEPEMFLRLICIENVLKDMNLPLFSNSETAPWKSGLSNSET--FSDGPLFFPNSQKTAQIELENVSNEISNLASNIKEKKKFTNKEINYRMINSNKTIQDSKR---ENKSMKYVEPPV 225          
The following BLAST results are available for this feature:
BLAST of SMED30021957 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. UniProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
gnl|BL_ORD_ID|203371011.640e-4138.86tr|A0A1S6KMK3|A0A1S6KMK3_SCHMD Uncharacterized pro... [more]
back to top
BLAST of SMED30021957 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30021957 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000039476.19.416e-16799.56SMESG000039476.1[more]
SMESG000039479.13.676e-4337.44SMESG000039479.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021957 ID=SMED30021957|Name=SMED30021957|organism=Schmidtea mediterranea sexual|type=transcript|length=976bp
TCTGCTGAATATAATTATTCTAATGAGACAATCTTAATTTGCTAATAAGC
GTTTTTTTTCTAACAAAGGAATGACACGGTCCACTGACAGCTCAATTAGA
CCAGAACAGTTTCAATGAAACTTATAATTATTATTTTACAGTTATCTCAA
ATCTATCTAATTAATACGTTTTCATTGCCGCTGTCTATCATGAAACTGAA
ACCATTTCAAAAACAACTTGGAAAAGTCAATCTTGATTACAATATTTCAA
ACGACGAATCGGTGCACAGCGGGCTGCGGCAGTTACTGAACACGACCAAT
CATTTATCAAACAAATCACAAATCGTTCATACTAAAGTCCTAATTCCGGG
TGATTTTCAAAACTTGATATCTCAATATCGAATATCTGATAGAATGCTGT
CGAATGCCGATTCTTCTATGATCGACGACCTTAACATTTATTGCAATCAG
TTAGGTTCGAATTTATGTTGGAGATGTTCACGGAAAATCGTTGACAACCG
ACTGAAAAGCGAAATCCACAAAGCTTTACCTAACCCGGATCCAGATATCC
TACCGAGACTGATTTGTGTAGAAAATGTGTTGAAGAACATGAATTTACCA
TTGTTTTCCAGTTCTGAAGTCGATGATTGGAACAACTGTAAATTAGATTC
AGGTGTCAACAAAATTTCTAATGAGCCTTTATTCTTTCCATATTTTAGTA
ATCCGGGAGACTCATTTAGTGCAGAAAGTTCGGAAATGAAAAAATATGAA
ACCAATGGCATGAGACATGTAACTTTTAATACTTCATTTATGGAGGAAGA
ACATGAAAAGCATCCTACACACCGACGGTCAATACAATTCATCAGTCCTC
CGGTTATAATGAAATAAGGACCTATTAGACACCACTATTGATTTCAGAAC
TTTATAAAATTAAATTAATTTCTATTACAATATAATTCATTTTTTATTAT
TTTTAAGACATGCATCTGATCACCAC
back to top

protein sequence of SMED30021957-orf-1

>SMED30021957-orf-1 ID=SMED30021957-orf-1|Name=SMED30021957-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=251bp
MKLIIIILQLSQIYLINTFSLPLSIMKLKPFQKQLGKVNLDYNISNDESV
HSGLRQLLNTTNHLSNKSQIVHTKVLIPGDFQNLISQYRISDRMLSNADS
SMIDDLNIYCNQLGSNLCWRCSRKIVDNRLKSEIHKALPNPDPDILPRLI
CVENVLKNMNLPLFSSSEVDDWNNCKLDSGVNKISNEPLFFPYFSNPGDS
FSAESSEMKKYETNGMRHVTFNTSFMEEEHEKHPTHRRSIQFISPPVIMK
*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000096ventral epidermis