SMED30008407

Overview
NameSMED30008407
Smed IDSMED30008407
Length (bp)1613
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 SMED30008407 (SMED30008407) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008407 (SMED30008407) 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 SMED30008407 (SMED30008407) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30008407 (SMED30008407) 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



SMED30008407

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
X2 cellSMED30008407 SmedASXL_015173SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
oocyteSMED30008407 Contig43773newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30008407 Contig43773newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30008407 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.010513:9616..11439 -7735
v31.000074:239215..240974 +5324
v31.002735:8503..10278 -5208
v31.011973:4112..5865 +5100
v31.000710:9020..10633 +5066
Homology
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BLAST of SMED30008407 vs. Planmine SMEST
Match: SMESG000044531.1 (SMESG000044531.1)

HSP 1 Score: 165.236 bits (417), Expect = 5.009e-49
Identity = 81/81 (100.00%), Postives = 81/81 (100.00%), Query Frame = 2 
Query: 1079 ARDFSMKNWNLLTFQYVGVLASVSGSFGEQFSEDLKAQKRTGSRGSRSQWTTLIGNSVSVPRTLSTLIKSSWRNYAHSSQF 1321
            ARDFSMKNWNLLTFQYVGVLASVSGSFGEQFSEDLKAQKRTGSRGSRSQWTTLIGNSVSVPRTLSTLIKSSWRNYAHSSQF
Sbjct:    6 ARDFSMKNWNLLTFQYVGVLASVSGSFGEQFSEDLKAQKRTGSRGSRSQWTTLIGNSVSVPRTLSTLIKSSWRNYAHSSQF 86
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BLAST of SMED30008407 vs. Planmine SMEST
Match: SMESG000043786.1 (SMESG000043786.1)

HSP 1 Score: 62.3882 bits (150), Expect = 4.126e-11
Identity = 25/35 (71.43%), Postives = 30/35 (85.71%), Query Frame = -1 
Query:    3 DFSHSEKPRSMTYTPTHVADRWRWAWERFRQEKCP 107
            + SHSEKP  MTY  TH+ADRWRWAWE+F+QE+CP
Sbjct:    2 NLSHSEKPSPMTYVSTHIADRWRWAWEQFQQERCP 36
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BLAST of SMED30008407 vs. Planmine SMEST
Match: SMESG000071285.1 (SMESG000071285.1)

HSP 1 Score: 58.9214 bits (141), Expect = 3.647e-10
Identity = 25/32 (78.12%), Postives = 28/32 (87.50%), Query Frame = -1 
Query:    3 HSEKPRSMTYTPTHVADRWRWAWERFRQEKCP 98
            +SEKP S +Y P H+ADRWRWAWERFRQEKCP
Sbjct:    7 YSEKPDSRSYVPIHMADRWRWAWERFRQEKCP 38
[Close]
BLAST of SMED30008407 vs. Planmine SMEST
Match: SMESG000018906.1 (SMESG000018906.1)

HSP 1 Score: 58.9214 bits (141), Expect = 3.923e-10
Identity = 24/34 (70.59%), Postives = 29/34 (85.29%), Query Frame = -1 
Query:    3 FSHSEKPRSMTYTPTHVADRWRWAWERFRQEKCP 104
              +SE+  SM YTPTH+ADRWRWAWE+FRQE+CP
Sbjct:    3 LPNSERSSSMAYTPTHIADRWRWAWEQFRQERCP 36
[Close]
BLAST of SMED30008407 vs. Planmine SMEST
Match: SMESG000047003.1 (SMESG000047003.1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.485e-9
Identity = 25/34 (73.53%), Postives = 28/34 (82.35%), Query Frame = -1 
Query:    3 FSHSEKPRSMTYTPTHVADRWRWAWERFRQEKCP 104
              +S +  SMTYTPTHVADRWRWAWE+FRQE CP
Sbjct:    3 LPYSGRSSSMTYTPTHVADRWRWAWEQFRQEICP 36
The following BLAST results are available for this feature:
BLAST of SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 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 SMED30008407 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044531.15.009e-49100.00SMESG000044531.1[more]
SMESG000043786.14.126e-1171.43SMESG000043786.1[more]
SMESG000071285.13.647e-1078.13SMESG000071285.1[more]
SMESG000018906.13.923e-1070.59SMESG000018906.1[more]
SMESG000047003.11.485e-973.53SMESG000047003.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008407 ID=SMED30008407|Name=SMED30008407|organism=Schmidtea mediterranea sexual|type=transcript|length=1613bp
TCGGGGCATTTCTCCTGCCGGAATCGTTCCCATGCCCATCTCCATCGATC
GGCGACGTGGGTTGGAGTATAAGTCATTGAACGGGGTTTCTCTGAATGCG
AAAAATCATTAGTAACACTGTATATTTATCTTTAATTGAATAATTTTAAA
AGGCAGAAACAAAATTCGAATTAAATCATTTGTGAAAACTATACTGAGGG
TCCTAAAACTATGCAATCAAAATATCAAAGGTTTTTACAGATCATTTAGT
CAAAATCGGCAAAAGTCCATGATCCAACTGGTGATCTCATTCTAATGGTT
GACCGAAATTATCAAAATTCAGATTTATAAACCGGTTTAGGTAACTTATT
TGGAAAAAAAAATCTAAATGTTATCGATTTCATAAGATTCACGGTTTGAA
AATTAGATTTTTTATAAATTATTTGAAAAAATTTCTAAGAGAGGTCAATT
TCTAATAAATTAAACTAAAATATGACTAAATTATCAATAAATTTATTTAC
CTTGTTTGACAAAATTCTAAAATCATGATTAAAATTAAACTCGTATAAAT
TATCTAGTAAAAATCCATAATAAATATCAATAAAATGTGATTAAATTGTC
AGTTAAACATACGCTTCTTACTTACCAAATCAAAGTTAAAGTTATATTGA
TTATCTAGTAAAAACTCGGGAGGGATTTATAAGTCAAAATATTCAAATAT
GATTAAATTATTATGTTTCTTTATATAACCTATTTAATTGTAAATTAAAG
AGAGGTAAATTCAAATTTTATTTAAATCGAAAACATTAACAAGTATATTG
TTACTTATATAATGATTGAAAAAAAAATTACCTGCTCTACATAAATTAAA
TTCCAGAAGCTCGACAGGGGTGGATGATTGATTCGCCGGCACTTCTTCGT
TGAGATTGAATCGTGAAAGCATGCAGTGTGGAATTACACCTCGTCGTATT
CTCTACCCCCCAGGTGTGTCTTTATATCCGGCTGGCATGTACAATTGTTG
TTCAGAATTCAGAATTTCAACACGACATGTGTGAAAATCTGGTTTATTAT
TATTCTGTGGAATTTACCATTTCTTAAGGCGCGGGATTTCAGCATGAAAA
ATTGGAACCTCTTAACATTTCAGTACGTGGGAGTTCTAGCGTCTGTTAGC
GGATCATTTGGCGAACAATTTTCGGAAGATCTTAAAGCGCAGAAAAGAAC
TGGCAGTCGCGGTTCGAGAAGTCAATGGACAACTTTAATCGGCAATTCTG
TTTCTGTCCCAAGAACCCTCTCAACTCTGATAAAATCGTCCTGGCGTAAT
TATGCACATTCATCTCAGTTTGTGATCAATATAATTCTTTCTTATTTGCT
TTATTTGGTGTTGGTTTCAATTTATGTAAATTATTTTTATTTATTAGGGC
CTACTTTGATATTTGATTGGCGATCCTTTCGTTTAATTTATGTTGGAAAT
TTAAAATCGTAAATTTGATGGCGGAAAGGGGTCGTAAGCCCATCGCAGAT
ATTCAGTATCAATTTTTCTCTCCTCTTTATTCTAATTAGGCAACAAGGTG
CTCTAAGTTCATGGTAGTTAGTTAAGTTTGTAATTTATTTACGGATCATC
TATTAGTGTGGGC
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protein sequence of SMED30008407-orf-1

>SMED30008407-orf-1 ID=SMED30008407-orf-1|Name=SMED30008407-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MKNWNLLTFQYVGVLASVSGSFGEQFSEDLKAQKRTGSRGSRSQWTTLIG
NSVSVPRTLSTLIKSSWRNYAHSSQFVINIILSYLLYLVLVSIYVNYFYL
LGPTLIFDWRSFRLIYVGNLKS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002111X2 cell