SMED30018535

Overview
NameSMED30018535
Smed IDSMED30018535
Length (bp)849
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 SMED30018535 (SMED30018535) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30018535 (SMED30018535) 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 SMED30018535 (SMED30018535) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30018535 (SMED30018535) 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
Homology
BLAST of SMED30018535 vs. Planmine SMEST
Match: SMESG000028986.1 (SMESG000028986.1)

HSP 1 Score: 278.485 bits (711), Expect = 2.799e-93
Identity = 134/136 (98.53%), Postives = 135/136 (99.26%), Query Frame = 1
Query:  379 DSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQKVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 786
            DSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKE+VDTLKNQLAQKDEALRSAEQK QDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL
Sbjct:  124 DSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEEVDTLKNQLAQKDEALRSAEQKAQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 259          
BLAST of SMED30018535 vs. Planmine SMEST
Match: SMESG000039707.1 (SMESG000039707.1)

HSP 1 Score: 281.567 bits (719), Expect = 3.248e-90
Identity = 133/145 (91.72%), Postives = 140/145 (96.55%), Query Frame = 1
Query:  352 KVNNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQKVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 786
            +V NEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKE++DTL+NQLAQKDEALRSAEQK ++LEKQV EWKL+DNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGI QMITGPS TPEGL
Sbjct:  111 EVKNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEEIDTLRNQLAQKDEALRSAEQKARELEKQVEEWKLKDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIRQMITGPSPTPEGL 255          
BLAST of SMED30018535 vs. Planmine SMEST
Match: SMESG000036802.1 (SMESG000036802.1)

HSP 1 Score: 284.263 bits (726), Expect = 1.188e-88
Identity = 133/147 (90.48%), Postives = 144/147 (97.96%), Query Frame = 1
Query:  346 KNKVNNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQKVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 786
            +++V NEFCLVDSHKKTLEQFRRD+AGYHQTAVTQTQRAEAM+RKCRYMEQTWLRPEKAIKLKE++DTLKN+LAQKDEALRSAEQK QDLE+QVAEWKLRDNIRTGLLQSGV+LSEEQQAIVLRNATGKDTGIGQ+ITGPS TPEGL
Sbjct:  684 RHEVKNEFCLVDSHKKTLEQFRRDVAGYHQTAVTQTQRAEAMIRKCRYMEQTWLRPEKAIKLKEEIDTLKNRLAQKDEALRSAEQKAQDLERQVAEWKLRDNIRTGLLQSGVNLSEEQQAIVLRNATGKDTGIGQLITGPSPTPEGL 830          
BLAST of SMED30018535 vs. Planmine SMEST
Match: SMESG000036802.1 (SMESG000036802.1)

HSP 1 Score: 284.263 bits (726), Expect = 1.904e-88
Identity = 133/147 (90.48%), Postives = 144/147 (97.96%), Query Frame = 1
Query:  346 KNKVNNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQKVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 786
            +++V NEFCLVDSHKKTLEQFRRD+AGYHQTAVTQTQRAEAM+RKCRYMEQTWLRPEKAIKLKE++DTLKN+LAQKDEALRSAEQK QDLE+QVAEWKLRDNIRTGLLQSGV+LSEEQQAIVLRNATGKDTGIGQ+ITGPS TPEGL
Sbjct:  734 RHEVKNEFCLVDSHKKTLEQFRRDVAGYHQTAVTQTQRAEAMIRKCRYMEQTWLRPEKAIKLKEEIDTLKNRLAQKDEALRSAEQKAQDLERQVAEWKLRDNIRTGLLQSGVNLSEEQQAIVLRNATGKDTGIGQLITGPSPTPEGL 880          
BLAST of SMED30018535 vs. Planmine SMEST
Match: SMESG000029751.1 (SMESG000029751.1)

HSP 1 Score: 253.832 bits (647), Expect = 3.054e-77
Identity = 126/151 (83.44%), Postives = 135/151 (89.40%), Query Frame = 1
Query:  334 VRLMKNKVNNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQTQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQKVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQMITGPSHTPEGL 786
            + L K K +N    +D HKKTLEQFRRDIAGYHQTAVT+TQRAEAMVRKCRYMEQTWLRPEKAIKLKE++DTL+NQLAQKDEALRSAEQKV +L KQV EWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDT I QMITG + TPEGL
Sbjct:  848 IDLFKKKQHNN-AQMDPHKKTLEQFRRDIAGYHQTAVTETQRAEAMVRKCRYMEQTWLRPEKAIKLKEEIDTLRNQLAQKDEALRSAEQKVLELGKQVEEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTDIRQMITGSAPTPEGL 997          
The following BLAST results are available for this feature:
BLAST of SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30018535 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 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 SMED30018535 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000028986.12.799e-9398.53SMESG000028986.1[more]
SMESG000039707.13.248e-9091.72SMESG000039707.1[more]
SMESG000036802.11.188e-8890.48SMESG000036802.1[more]
SMESG000036802.11.904e-8890.48SMESG000036802.1[more]
SMESG000029751.13.054e-7783.44SMESG000029751.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018535 ID=SMED30018535|Name=SMED30018535|organism=Schmidtea mediterranea sexual|type=transcript|length=849bp
ATGAAGAAGGATATTCCTGATTTAATCGATAGTGGTGCGTTTCCGTTGGT
CAACTGTCCGTTGGGTTTAAACAAATATTATCGTGAAAATGATTTGGTTC
TTTCTCACCGTGATTTAAGCTATTCCTATCAATGTCGATTGAATTTAATA
ATGCTGCAAGGTTGTTTACTAACGATTTATATTAATTACAATCCCTCGAA
TAAACATACCGTTATCAATTTACTTCTAAAATTGAGAAACGAGGAAGCAG
CCAGAGACTTCTTCCTTATTTCTCTTTTCAGCTATAGGGAGAAACGAAAT
CTTTACCATCATTTATTTCGAAAAAACGAAAAGGTAAGACTAATGAAAAA
TAAAGTTAATAATGAATTTTGTTTAGTGGACTCTCACAAGAAAACTCTGG
AACAATTCCGAAGGGATATAGCCGGTTACCATCAAACCGCAGTAACACAA
ACGCAGAGGGCAGAGGCCATGGTGAGGAAGTGTCGCTACATGGAGCAGAC
ATGGCTCCGCCCCGAGAAGGCAATCAAGCTAAAAGAAAAGGTCGACACAT
TGAAGAATCAATTAGCTCAGAAGGATGAAGCCCTGCGGTCGGCCGAACAG
AAGGTCCAGGATCTAGAAAAACAGGTCGCAGAGTGGAAGTTGAGAGACAA
CATCCGGACAGGCCTCCTGCAGAGTGGTGTTCACCTATCCGAAGAACAGC
AGGCGATAGTGCTAAGGAATGCCACAGGTAAAGACACTGGCATTGGACAG
ATGATAACAGGTCCGTCACATACACCGGAAGGATTGCCAAAGAAAAACCG
CAGAAAGAACCGACCCAACAAAAGAGAAAGGGAGCGACAGGCCAGAGTA
back to top

protein sequence of SMED30018535-orf-1

>SMED30018535-orf-1 ID=SMED30018535-orf-1|Name=SMED30018535-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=283bp
MKKDIPDLIDSGAFPLVNCPLGLNKYYRENDLVLSHRDLSYSYQCRLNLI
MLQGCLLTIYINYNPSNKHTVINLLLKLRNEEAARDFFLISLFSYREKRN
LYHHLFRKNEKVRLMKNKVNNEFCLVDSHKKTLEQFRRDIAGYHQTAVTQ
TQRAEAMVRKCRYMEQTWLRPEKAIKLKEKVDTLKNQLAQKDEALRSAEQ
KVQDLEKQVAEWKLRDNIRTGLLQSGVHLSEEQQAIVLRNATGKDTGIGQ
MITGPSHTPEGLPKKNRRKNRPNKRERERQARV
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000074oocyte
PLANA:0000231vitelline gland