SMED30023817

Overview
NameSMED30023817
Smed IDSMED30023817
Length (bp)464
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30023817 (SMED30023817) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30023817 (SMED30023817) 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.
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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



SMED30023817

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
Smed sexual biotypeSMED30023817h1SMcG0022520 Contig44698newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30023817h1SMcG0022520 Contig44698uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30023817h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023817h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023817h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023817h1SMcG0022520 dd_Smed_v4_15048_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30023817 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 296.975 bits (759), Expect = 7.768e-96
Identity = 151/154 (98.05%), Postives = 153/154 (99.35%), Query Frame = 2 
Query:    2 QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPXXXXXXXXXXXXXYFGCSKEPHEQIPLI 463
            QYGLNNQEDRN+WQSFMVRICKNDVGFKSVPM+EAWLMRHMS HFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI
Sbjct:  265 QYGLNNQEDRNAWQSFMVRICKNDVGFKSVPMKEAWLMRHMSGHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI 418
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BLAST of SMED30023817 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 296.975 bits (759), Expect = 7.902e-96
Identity = 151/154 (98.05%), Postives = 153/154 (99.35%), Query Frame = 2 
Query:    2 QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPXXXXXXXXXXXXXYFGCSKEPHEQIPLI 463
            QYGLNNQEDRN+WQSFMVRICKNDVGFKSVPM+EAWLMRHMS HFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI
Sbjct:  271 QYGLNNQEDRNAWQSFMVRICKNDVGFKSVPMKEAWLMRHMSGHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI 424
[Close]
BLAST of SMED30023817 vs. Planmine SMEST
Match: SMESG000016292.1 (SMESG000016292.1)

HSP 1 Score: 296.975 bits (759), Expect = 1.395e-95
Identity = 151/154 (98.05%), Postives = 153/154 (99.35%), Query Frame = 2 
Query:    2 QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPXXXXXXXXXXXXXYFGCSKEPHEQIPLI 463
            QYGLNNQEDRN+WQSFMVRICKNDVGFKSVPM+EAWLMRHMS HFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI
Sbjct:  265 QYGLNNQEDRNAWQSFMVRICKNDVGFKSVPMKEAWLMRHMSGHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQIPLI 418
[Close]
BLAST of SMED30023817 vs. Planmine SMEST
Match: SMESG000016303.1 (SMESG000016303.1)

HSP 1 Score: 198.749 bits (504), Expect = 1.047e-59
Identity = 100/154 (64.94%), Postives = 115/154 (74.68%), Query Frame = 2 
Query:    2 QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPXXXXXXXXXXXXXYFGCSKEPHEQIPLI 463
            QYGLNNQEDRN+WQSFM+RICKND+GFK  P     +MR M S  Y  G+I   DY L+   DEA +N  WFH+T HLPT HF + QKINFGCYIGKRPRSISDN+FW +TNVLY+N L DVIFD NK IK + KN N+ FGC  + HEQIPLI
Sbjct:  248 QYGLNNQEDRNAWQSFMLRICKNDLGFKYTPTLLGNVMRQMVSLKYIAGTINNLDYILASFPDEASYNSSWFHDTAHLPTTHFITPQKINFGCYIGKRPRSISDNFFWSETNVLYINKLADVIFDLNKVIKLRIKNTNELFGCKNQTHEQIPLI 401
[Close]
BLAST of SMED30023817 vs. Planmine SMEST
Match: SMESG000016303.1 (SMESG000016303.1)

HSP 1 Score: 198.749 bits (504), Expect = 1.151e-59
Identity = 100/154 (64.94%), Postives = 115/154 (74.68%), Query Frame = 2 
Query:    2 QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGSIGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPRSISDNYFWGQTNVLYLNMLVDVIFDPXXXXXXXXXXXXXYFGCSKEPHEQIPLI 463
            QYGLNNQEDRN+WQSFM+RICKND+GFK  P     +MR M S  Y  G+I   DY L+   DEA +N  WFH+T HLPT HF + QKINFGCYIGKRPRSISDN+FW +TNVLY+N L DVIFD NK IK + KN N+ FGC  + HEQIPLI
Sbjct:  247 QYGLNNQEDRNAWQSFMLRICKNDLGFKYTPTLLGNVMRQMVSLKYIAGTINNLDYILASFPDEASYNSSWFHDTAHLPTTHFITPQKINFGCYIGKRPRSISDNFFWSETNVLYINKLADVIFDLNKVIKLRIKNTNELFGCKNQTHEQIPLI 400
The following BLAST results are available for this feature:
BLAST of SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 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 SMED30023817 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000016292.17.768e-9698.05SMESG000016292.1[more]
SMESG000016292.17.902e-9698.05SMESG000016292.1[more]
SMESG000016292.11.395e-9598.05SMESG000016292.1[more]
SMESG000016303.11.047e-5964.94SMESG000016303.1[more]
SMESG000016303.11.151e-5964.94SMESG000016303.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023817 ID=SMED30023817|Name=SMED30023817|organism=Schmidtea mediterranea sexual|type=transcript|length=464bp
TCAGTACGGTTTGAATAATCAAGAAGATCGAAACTCTTGGCAGAGCTTTA
TGGTGAGAATATGCAAGAATGATGTTGGATTTAAGTCAGTTCCAATGGAG
GAGGCCTGGTTGATGAGACACATGTCCAGTCATTTCTATAACATTGGATC
CATAGGTGAATTTGATTATACTTTGTCCCCTACCCATGATGAAGCAGGTC
ACAATCCGGATTGGTTTCACAACACTGTTCATTTACCAACGAAACATTTT
ACTTCTTCACAAAAGATCAACTTTGGCTGTTATATCGGTAAAAGACCTCG
TTCAATCAGTGATAACTACTTTTGGGGTCAAACAAATGTCTTGTATTTAA
ACATGCTAGTCGACGTTATATTCGATCCAAATAAGACCATCAAATTCAAA
ACCAAAAATAACAACAAATATTTCGGCTGTTCCAAGGAACCCCATGAACA
AATTCCTCTGATAG
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protein sequence of SMED30023817-orf-1

>SMED30023817-orf-1 ID=SMED30023817-orf-1|Name=SMED30023817-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=154bp
QYGLNNQEDRNSWQSFMVRICKNDVGFKSVPMEEAWLMRHMSSHFYNIGS
IGEFDYTLSPTHDEAGHNPDWFHNTVHLPTKHFTSSQKINFGCYIGKRPR
SISDNYFWGQTNVLYLNMLVDVIFDPNKTIKFKTKNNNKYFGCSKEPHEQ
IPLI
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell