SMED30022070

Overview
NameSMED30022070
Smed IDSMED30022070
Length (bp)1478
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 SMED30022070 (SMED30022070) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30022070 (SMED30022070) 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 SMED30022070 (SMED30022070) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30022070 (SMED30022070) 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




SMED30022070

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30022070 SmedASXL_016243SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
pharynxSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult colorimetric in situ hybridization evidence
muscle cellSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v4_6854_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30022070 dd_Smed_v4_19369_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30022070SMESG000067158.1 SMESG000079384.1 SMESG000006522.1 dd_Smed_v6_6854_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
non-ciliated epidermisSMED30022070 dd_Smed_v4_19369_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
Homology
BLAST of SMED30022070 vs. Planmine SMEST
Match: SMESG000058203.1 (SMESG000058203.1)

HSP 1 Score: 58.5362 bits (140), Expect = 2.192e-9
Identity = 31/41 (75.61%), Postives = 31/41 (75.61%), Query Frame = 1
Query:  508 FPLYGII------IDVSATAFSRRSLHGHELLAIIHALTQF 612
             PLY  I      IDVSA AFSRRSLHGHELLAIIHALTQF
Sbjct:   10 LPLYLPISPITDDIDVSAPAFSRRSLHGHELLAIIHALTQF 50          
BLAST of SMED30022070 vs. Planmine SMEST
Match: SMESG000079384.1 (SMESG000079384.1)

HSP 1 Score: 46.9802 bits (110), Expect = 6.368e-6
Identity = 22/22 (100.00%), Postives = 22/22 (100.00%), Query Frame = -2
Query: 1301 RYNSQSDSDQDMRLNLSVIYQV 1366
            RYNSQSDSDQDMRLNLSVIYQV
Sbjct:  135 RYNSQSDSDQDMRLNLSVIYQV 156          
BLAST of SMED30022070 vs. Planmine SMEST
Match: SMESG000003001.1 (SMESG000003001.1)

HSP 1 Score: 47.3654 bits (111), Expect = 7.448e-6
Identity = 21/26 (80.77%), Postives = 21/26 (80.77%), Query Frame = 2
Query:  590 LYTHLHSSIVCFIFLSCVMFWLWATK 667
            L  HLHSSIVCFI LSC MFWLWA K
Sbjct:  188 LTPHLHSSIVCFILLSCDMFWLWAEK 213          
The following BLAST results are available for this feature:
BLAST of SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 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 SMED30022070 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000058203.12.192e-975.61SMESG000058203.1[more]
SMESG000079384.16.368e-6100.00SMESG000079384.1[more]
SMESG000003001.17.448e-680.77SMESG000003001.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022070 ID=SMED30022070|Name=SMED30022070|organism=Schmidtea mediterranea sexual|type=transcript|length=1478bp
TTAATTTAACGTTTAGTCCCTCGTCCTATTAAGGTAATTAACATATTTCG
TATTCACTCGTGGCTAGTATGTCTCCTTCTAGTTTGTACAAGGGTGATTA
TCGATATGGCGCTGACTCTTATAACTAAATTTACATGATCATCTCATTTT
TGGGTCGGGGTTTTAAAATTTTTCTCTGTAGTTGCCGGAATTTATGACAT
TGTGAAGTTTGTCGTATTAGTACAGTGACTATTCAACTTAAAATCTGGGT
TTGGAAATTTAAATCAATTATTTCAGTCTGTTATTTATATGAGTTATCGA
CATATCAACAATTTCTCCACATAAATTTCCCCGTCACCTTCCCATAGTTA
ATCTTAGGATAAAATTGTGTCAATATTAAGAGTTTATGAGTGCCCACTGG
AAAACACAGTGTTTTGATTTTAAGCCGTTTGTTATTGTAATTTAGGTCGA
GTTTTCAGGAAAATCATGATGATGGACTAGCCAAAAGACTATTCCCTCTT
CAACCCATTTCCCCTATACGGAATAATAATTGACGTTTCAGCTACTGCGT
TCTCACGCCGTAGCCTTCACGGGCACGAATTATTGGCGATTATACACGCA
CTTACACAGTTCGATAGTGTGTTTTATTTTTCTATCTTGCGTTATGTTTT
GGCTGTGGGCCACCAAAAATAAAATAATAGAAAAAATAAATTACCAAATG
AATTAGGCAAAAATCTCGACGCATAAACTGTATATTTAGCATTCATATAA
ACAAATTTTTAATCGGGCATCGATGCACATCCGGAATGAAGATCCACCAA
AAGACAAAAGGTTAAAAAAATTGATAATTAGTCCAGCTGACCAAACTAAT
AGCCAATATACCGCAGAATACCAAAATGCCTACCACGTGACTAATACTAA
TTACGATGAAAAATTTACGATGTTTCTGAAAAATTTGAAACAAAATCCCA
TAAAAAGAGAATCGCTTCTTAGTGATAAAGATAATTTCCGGAATAAAGAT
AACGTGACCAATATTGATTGCTGTGACAAATTCCGGAATATATATCCAGC
CTACCACGTGACTTTCTGTGGCTTCTGTGGCAGAAATATTTCTGATCGAA
ACATGATAACAGCTGTTATGAAGGCAACCTATGAACCTTATGAACGCCAC
AGTGTGAGCACATACACTAGACCTTACCACAGAGACCCACCGCAGAATTA
TCAAGCAGAATATAAATTGCAGGAGTGCGATTTCAAATATTGTTAACTGA
TATATATGAACGGGACAGGAAAATAGATTTTGTTAAAAATACAAAATTTT
AACCTGATATATAACTGATAAATTCAACCGCATATCCTGATCTGAATCTG
ATTGGCTGTTATATCTCAATATTAATTATAATAACAATTATTAGTGCATA
TCCACAATAAAGTTATACAAAACGCGCTTTATAATATTTCAAATTTCAAA
ATATATTTATTATTATTTATTTTTATTA
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protein sequence of SMED30022070-orf-1

>SMED30022070-orf-1 ID=SMED30022070-orf-1|Name=SMED30022070-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=158bp
MHIRNEDPPKDKRLKKLIISPADQTNSQYTAEYQNAYHVTNTNYDEKFTM
FLKNLKQNPIKRESLLSDKDNFRNKDNVTNIDCCDKFRNIYPAYHVTFCG
FCGRNISDRNMITAVMKATYEPYERHSVSTYTRPYHRDPPQNYQAEYKLQ
ECDFKYC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0002063non-ciliated epidermis
PLANA:0003001lateral region of the whole animal