SMED30009662

Overview
NameSMED30009662
Smed IDSMED30009662
Length (bp)604
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 SMED30009662 (SMED30009662) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009662 (SMED30009662) 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 SMED30009662 (SMED30009662) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009662 (SMED30009662) 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



SMED30009662

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
head regionSMED30009662h1SMcG0017131 SmedASXL_011884SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30009662h1SMcG0017131 SmedASXL_011884SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30009662h1SMcG0017132 SmedASXL_011883SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30009662h1SMcG0017132 SmedASXL_011883SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30009662h1SMcG0017131 dd_Smed_v4_566_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30009662h1SMcG0017131 dd_Smed_v6_566_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009662 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006828:2822..3402 -2688
v31.006828:7142..7722 -2679
v31.014929:13157..13741 +2024
Homology
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BLAST of SMED30009662 vs. Planmine SMEST
Match: SMESG000061321.1 (SMESG000061321.1)

HSP 1 Score: 174.481 bits (441), Expect = 4.692e-56
Identity = 118/121 (97.52%), Postives = 119/121 (98.35%), Query Frame = 1 
Query:  142 MYVNGFVDLRLLTGLKLNVEGLIKADXXXXXXXXXXXXNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIXXXXXXXXXXXXXXXTHFPDQD 504
            MYVNGFVDLRLLTGLKLNV GLIKADLGLRLGLYLGAG YRSVLEIPAINHFL+GLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD
Sbjct:    1 MYVNGFVDLRLLTGLKLNVAGLIKADLGLRLGLYLGAGYYRSVLEIPAINHFLIGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD 121
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BLAST of SMED30009662 vs. Planmine SMEST
Match: SMESG000061323.1 (SMESG000061323.1)

HSP 1 Score: 173.711 bits (439), Expect = 1.197e-55
Identity = 117/121 (96.69%), Postives = 118/121 (97.52%), Query Frame = 1 
Query:  142 MYVNGFVDLRLLTGLKLNVEGLIKADXXXXXXXXXXXXNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIXXXXXXXXXXXXXXXTHFPDQD 504
            MYVNGFVDLRLLTGLKLNV GLIK DLGLRLGLYLGAG YRSVLEIPAINHFL+GLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD
Sbjct:    1 MYVNGFVDLRLLTGLKLNVAGLIKTDLGLRLGLYLGAGYYRSVLEIPAINHFLIGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD 121
[Close]
BLAST of SMED30009662 vs. Planmine SMEST
Match: SMESG000061319.1 (SMESG000061319.1)

HSP 1 Score: 177.563 bits (449), Expect = 6.094e-55
Identity = 118/121 (97.52%), Postives = 119/121 (98.35%), Query Frame = 1 
Query:  142 MYVNGFVDLRLLTGLKLNVEGLIKADXXXXXXXXXXXXNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIXXXXXXXXXXXXXXXTHFPDQD 504
            MYVNGFVDLRLLTGLKLNV GLIKADLGLRLGLYLGAG YRSVLEIPAINHFL+GLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD
Sbjct:    1 MYVNGFVDLRLLTGLKLNVAGLIKADLGLRLGLYLGAGYYRSVLEIPAINHFLIGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD 121
[Close]
BLAST of SMED30009662 vs. Planmine SMEST
Match: SMESG000061320.1 (SMESG000061320.1)

HSP 1 Score: 142.895 bits (359), Expect = 1.233e-43
Identity = 101/119 (84.87%), Postives = 105/119 (88.24%), Query Frame = 1 
Query:  148 VNGFVDLRLLTGLKLNVEGLIKADXXXXXXXXXXXXNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIXXXXXXXXXXXXXXXTHFPDQD 504
               F   +   G ++   GLIKADLGLRLGLYLGAG YRSVLEIPAINHFL+GLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD
Sbjct:    4 CEWFCGSQTFDGTEIECGGLIKADLGLRLGLYLGAGYYRSVLEIPAINHFLIGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQIRKLERRRYELEALRRTHFPDQD 122

HSP 2 Score: 54.299 bits (129), Expect = 1.892e-9
Identity = 22/22 (100.00%), Postives = 22/22 (100.00%), Query Frame = 3 
Query:  138 MHVCEWFCGSQTFDGTEIECGG 203
            MHVCEWFCGSQTFDGTEIECGG
Sbjct:    1 MHVCEWFCGSQTFDGTEIECGG 22
[Close]
BLAST of SMED30009662 vs. Planmine SMEST
Match: SMESG000061337.1 (SMESG000061337.1)

HSP 1 Score: 137.502 bits (345), Expect = 1.236e-41
Identity = 82/99 (82.83%), Postives = 93/99 (93.94%), Query Frame = 1 
Query:  142 MYVNGFVDLRLLTGLKLNVEGLIKADXXXXXXXXXXXXNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGLGIDREKINRLVYQI 438
            MYVNG + LRLLTGLKLNV+GLIKADLGLRLGLYLGAGNYRSVLEIPAIN+FLLGLRARV+GPIYA V+AHLE+IG+ISSG+YGLGIDRE ++ LV+ I
Sbjct:    1 MYVNGILGLRLLTGLKLNVDGLIKADLGLRLGLYLGAGNYRSVLEIPAINNFLLGLRARVAGPIYAEVKAHLEEIGQISSGMYGLGIDRETVDNLVHHI 99
The following BLAST results are available for this feature:
BLAST of SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 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 SMED30009662 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000061321.14.692e-5697.52SMESG000061321.1[more]
SMESG000061323.11.197e-5596.69SMESG000061323.1[more]
SMESG000061319.16.094e-5597.52SMESG000061319.1[more]
SMESG000061320.11.233e-4384.87SMESG000061320.1[more]
SMESG000061337.11.236e-4182.83SMESG000061337.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009662 ID=SMED30009662|Name=SMED30009662|organism=Schmidtea mediterranea sexual|type=transcript|length=604bp
TTGCAAGTAAGGAAGGAATACAAATTGAGAACTTAAACTGACAGACCAAA
ACAAAATTATTCTATAAAAGCGATCATAAATTAGTTTTTTTCAGTCATGA
ATTTGAAATTATCTCTTTTAATACTTTCTTGCTTCACATGCATGTATGTG
AATGGTTTTGTGGATCTCAGACTTTTGACGGGACTGAAATTGAATGTGGA
GGGCCTCATTAAGGCTGACTTGGGATTAAGATTGGGTCTGTACTTGGGAG
CCGGCAATTATCGATCAGTATTAGAGATCCCGGCAATCAATCATTTTCTA
CTTGGACTCAGGGCCCGTGTATCGGGTCCAATCTATGCAAATGTACAAGC
ACATTTGGAAGACATTGGAAAAATATCAAGTGGAATTTACGGTTTAGGCA
TTGACAGAGAAAAGATCAACAGATTAGTTTATCAAATAAGAAAACTTGAA
CGAAGACGATACGAATTAGAAGCATTACGACGAACTCATTTCCCTGACCA
AGATGTAAACAAAGTGTTTGAAAAATGTTGTGTGGAAGTTGTCGAAGAAT
CGAGTAATGAAAAATGATTTAGTGAATAAATGTGAAATTTTTCATATTTA
TTCT
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protein sequence of SMED30009662-orf-1

>SMED30009662-orf-1 ID=SMED30009662-orf-1|Name=SMED30009662-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=157bp
MNLKLSLLILSCFTCMYVNGFVDLRLLTGLKLNVEGLIKADLGLRLGLYL
GAGNYRSVLEIPAINHFLLGLRARVSGPIYANVQAHLEDIGKISSGIYGL
GIDREKINRLVYQIRKLERRRYELEALRRTHFPDQDVNKVFEKCCVEVVE
ESSNEK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region