SMED30013781

Overview
NameSMED30013781
Smed IDSMED30013781
Length (bp)2482
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 SMED30013781 (SMED30013781) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013781 (SMED30013781) 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 SMED30013781 (SMED30013781) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013781 (SMED30013781) 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
[Close]
BLAST of SMED30013781 vs. Planmine SMEST
Match: SMESG000024369.1 (SMESG000024369.1)

HSP 1 Score: 257.684 bits (657), Expect = 7.767e-81
Identity = 128/177 (72.32%), Postives = 140/177 (79.10%), Query Frame = 1 
Query: 1453 MMNLPYSGKFGPMVYVPTHVADRWRQAWRHYSQDRCPELHQSGPRLAEGRSEGGNVTSGLADQPWEEWSPDWEIREHARHLLGRLESHQREVDVQVIRTRQYLTNIEEDISASRIANVYHHPPQGKAPRNHTGGRPNNYQEDSNRPRVTRVRNTK*PVMISSNCSLEEWVERGFTDS 1983
            MMNLPYS K GPMVYVPTHVADRWRQAWR +SQDRCPE  +   R    ++   N    L+DQPW+EWSP WEIREHARHLLGRLES QR +DVQVIR RQYL NIEEDISA RIAN+Y HPPQ KAP NH G R N++QE+ NR +VTRV NTK  VMISSNCS EEWVERGFTDS
Sbjct:    1 MMNLPYSEKSGPMVYVPTHVADRWRQAWRQFSQDRCPEFPRPESRQFNWQAGESNCNPWLSDQPWKEWSPAWEIREHARHLLGRLESRQRRLDVQVIRARQYLANIEEDISAGRIANIYRHPPQYKAPLNHAGRRTNDHQENPNRSKVTRVCNTKRAVMISSNCSPEEWVERGFTDS 177
[Close]
BLAST of SMED30013781 vs. Planmine SMEST
Match: SMESG000007882.1 (SMESG000007882.1)

HSP 1 Score: 253.447 bits (646), Expect = 2.571e-79
Identity = 124/176 (70.45%), Postives = 141/176 (80.11%), Query Frame = 1 
Query: 1453 MMNLPYSGKFGPMVYVPTHVADRWRQAWRHYSQDRCPELHQSGPRLAEGRSEGGNVTSGLADQPWEEWSPDWEIREHARHLLGRLESHQREVDVQVIRTRQYLTNIEEDISASRIANVYHHPPQGKAPRNHTGGRPNNYQEDSNRPRVTRVRNTK*PVMISSNCSLEEWVERGFTD 1980
            MM+LPYS + GPMVYVPTHVADRWRQAW  +SQDRCPE  +   R    ++E GN    L++QPWEEWSP WEIREHARHLLGRLESHQR+VD+QVIR RQYL NIEEDISA RIAN+Y HP   +AP NH GG+ N++QED NRP VTRV NTK PVMIS+NCS EE VERGFT+
Sbjct:    1 MMDLPYSERSGPMVYVPTHVADRWRQAWSQFSQDRCPEFSRPESRQFNRQTEEGNGNPWLSNQPWEEWSPAWEIREHARHLLGRLESHQRQVDIQVIRARQYLANIEEDISAGRIANIYRHPLHHQAPINHAGGKSNDHQEDPNRPNVTRVCNTKRPVMISTNCSPEECVERGFTN 176
[Close]
BLAST of SMED30013781 vs. Planmine SMEST
Match: SMESG000014158.1 (SMESG000014158.1)

HSP 1 Score: 254.218 bits (648), Expect = 4.006e-78
Identity = 125/169 (73.96%), Postives = 138/169 (81.66%), Query Frame = 1 
Query: 1477 KFGPMVYVPTHVADRWRQAWRHYSQDRCPELHQSGPRLAEGRSEGGNVTSGLADQPWEEWSPDWEIREHARHLLGRLESHQREVDVQVIRTRQYLTNIEEDISASRIANVYHHPPQGKAPRNHTGGRPNNYQEDSNRPRVTRVRNTK*PVMISSNCSLEEWVERGFTDS 1983
            K GPMVYVP+HVADRWRQAWR +SQDRCPEL +   R    +S   N    L+DQ WEEWSP WEIREHARHLLGRLE+HQR+VDVQVIR+RQYL NIEEDISA RIANVY HPPQ KAP N+TGG+ N++QED  RP+VTRVRNTK PVMI  NCS EEWVERGFTDS
Sbjct:  104 KSGPMVYVPSHVADRWRQAWRQFSQDRCPELSRPESRQLSWQSGESNHNPWLSDQQWEEWSPAWEIREHARHLLGRLENHQRQVDVQVIRSRQYLANIEEDISAGRIANVYCHPPQDKAPLNYTGGKTNDHQEDPTRPKVTRVRNTKRPVMIFFNCSPEEWVERGFTDS 272
[Close]
BLAST of SMED30013781 vs. Planmine SMEST
Match: SMESG000006077.1 (SMESG000006077.1)

HSP 1 Score: 244.202 bits (622), Expect = 8.513e-76
Identity = 123/177 (69.49%), Postives = 138/177 (77.97%), Query Frame = 1 
Query: 1453 MMNLPYSGKFGPMVYVPTHVADRWRQAWRHYSQDRCPELHQSGPRLAEGRSEGGNVTSGLADQPWEEWSPDWEIREHARHLLGRLESHQREVDVQVIRTRQYLTNIEEDISASRIANVYHHPPQGKAPRNHTGGRPNNYQEDSNRPRVTRVRNTK*PVMISSNCSLEEWVERGFTDS 1983
            MM LPYS K GPMVYVP HVADRWR+AWR +SQDR PE  +   R    ++  GN    L++Q  EEWSP WEIREHARHLLGRLESHQR+VDVQVIR RQYL NIEEDI+A RIAN+Y HP   +AP NH G + N++QED NRP VTRVRNTK PVMIS+NCS EEWVERGFTDS
Sbjct:    1 MMGLPYSEKSGPMVYVPIHVADRWRKAWRQFSQDRDPEFVRLESRQFNWQTGEGNGNPWLSNQQCEEWSPVWEIREHARHLLGRLESHQRQVDVQVIRARQYLANIEEDIAAGRIANIYRHPLHHQAPLNHAGEKSNDHQEDPNRPNVTRVRNTKRPVMISTNCSPEEWVERGFTDS 177
[Close]
BLAST of SMED30013781 vs. Planmine SMEST
Match: SMESG000047003.1 (SMESG000047003.1)

HSP 1 Score: 216.083 bits (549), Expect = 1.854e-65
Identity = 108/176 (61.36%), Postives = 125/176 (71.02%), Query Frame = 1 
Query: 1456 MNLPYSGKFGPMVYVPTHVADRWRQAWRHYSQDRCPELHQSGPRLAEGRSEGGNVTSGLADQPWEEWSPDWEIREHARHLLGRLESHQREVDVQVIRTRQYLTNIEEDISASRIANVYHHPPQGKAPRNHTGGRPNNYQEDSNRPRVTRVRNTK*PVMISSNCSLEEWVERGFTDS 1983
            M LPYSG+   M Y PTHVADRWR AW  + Q+ CPE  Q  P+  +GRS   +  S LAD+ WEEWSP WEIRE ARHLLGRLE+HQR+VD+QV+R RQYL N+EED+ A RIA+ YHHPPQ KAP              SN+P++TR RNTK PVMI SNCS EEWVERGF DS
Sbjct:    1 MALPYSGRSSSMTYTPTHVADRWRWAWEQFRQEICPEFPQPEPQQFDGRSMESDHNSWLADRQWEEWSPAWEIREQARHLLGRLENHQRQVDLQVVRARQYLANVEEDLLAGRIASSYHHPPQYKAPL-------------SNQPKITRARNTKRPVMIISNCSPEEWVERGFKDS 163
The following BLAST results are available for this feature:
BLAST of SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 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 SMED30013781 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000024369.17.767e-8172.32SMESG000024369.1[more]
SMESG000007882.12.571e-7970.45SMESG000007882.1[more]
SMESG000014158.14.006e-7873.96SMESG000014158.1[more]
SMESG000006077.18.513e-7669.49SMESG000006077.1[more]
SMESG000047003.11.854e-6561.36SMESG000047003.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013781 ID=SMED30013781|Name=SMED30013781|organism=Schmidtea mediterranea sexual|type=transcript|length=2482bp
AAAAAAATTAAGAAATTTAAAAACCATAATACAAATCCTTACTCACGATG
ATCATTCAGCGGAGATAAATTTCATAAACTCTGAAATTTACCAAGTTAGT
AAATATAGGAAATTAGAAACTTGACACCTACATAAATCGATAATTCGCGA
GAAAGTTGGTGAATAACAAGCTTGTCATTGCACCACACACCCGCAGTAAT
CAGCTAGTTCTCTCTAGCAATGTGGTAATTATGCACACCTACCTTTTTCT
CTTCCCCAAACTATATAAGAAAAATAGACTAATCAATAATCAAAACGAAT
TTTTGCTCCGAGAAATTAAAATGTCTTACCAGCCAACTGACTACAACGAG
AAGCCGACCGATAAGTCACCCGATGAGGTCGGAGATGTGGAATTAGAAAT
CCGCCATTCAAGTAAATTTTCTTATAATGTGGTTTAATTTTGACAAGATT
GATTAACGTATATTATCCTATTTGTTCATCAAAAAATAATTTTTTAATTT
TAAAAGAATTGCATTTTTATATTTTGTTTATATAAATACTTGTTGATTTA
AAATATTTATTGTTTTTTTATTTTTAAAAATAGTAGACATTTATTATTGA
ACCTTTATTGAAAATATGATTTAAAATATAAGAAATTTCGGATATACTTT
GGGTTTAAGAATTGTTGCCTTTTAATATTCATTTAGTAGATATTTCTACA
ACAGGAGGGGTTTAGTTCATTTCAATTTCACTATAATGGCCAGCTCATTA
GGTACGATTAGATAGAGCACTCCGATTGAAGATGGGTACTTCGGGATATG
TTAATAAGAACTGGGGATGCGCTGTACCTATAAACCTCATTTAACTAAAT
AAAAGTACGCCTAGTTCACATCGTAACATTACTTTATTTATAACAAAAGG
AATAACTAAATGTGTCTAACTCGATATTATAATAGGAATCGGATTTATCA
ATGTCATATTTAAGTTTTGCTGTTTTTCAGAATTTAGTAAATTTTTAGGG
GGAAGTTCGCATGTGCACAGGTGTATTTCCGCTTTATAATTTTTGTACTT
CATTACTCTACCTAGTAGAATTTTCGTTTATACCAATTGGAAATAACTGT
GGTAAGAGTAGCTCATGGTAAATTTAGTGAATATTTTAATAGAAAATTTA
TTAAATAATTTTAATCATAAAAATACGGTTTTTTCCCAAATAGTTTCATT
AAAATGAACATTTAATTTTATACACGGATATAGATATATACGTATATGTT
AAAAATTTGTTAAAATGTTATAATTAGTCGTTTTGGCATGTTTCGTTTTG
TGAATCCAATGGTGTACCATGTAATGAAACGATACATTTTACCAAGATAT
TTTTAACCCGCAGGTAAGTCGATGAGTTGTATAAATTATCGGTTACCTAT
ATTTTTTTTTATTATAAAAGATGCTAGATTTTGGAACAAATGTATAATGA
TAATGATGAATCTTCCTTATTCAGGAAAATTCGGGCCGATGGTCTATGTC
CCTACCCACGTTGCCGATCGATGGAGGCAAGCGTGGAGACATTACAGCCA
GGACAGGTGCCCCGAGCTCCACCAATCCGGACCTCGACTGGCTGAAGGAC
GATCGGAGGGAGGTAATGTTACTTCCGGGTTAGCTGACCAACCATGGGAG
GAGTGGAGTCCGGATTGGGAGATCCGCGAACATGCTCGCCATCTCCTTGG
TCGCCTCGAAAGCCACCAACGAGAAGTAGACGTACAGGTGATCCGGACCC
GCCAATACTTGACGAACATCGAGGAGGACATCTCGGCCAGCCGGATTGCC
AACGTCTACCACCACCCACCTCAAGGCAAGGCCCCACGTAATCATACTGG
CGGGAGGCCCAACAACTACCAGGAGGACTCCAACAGGCCCAGAGTCACTC
GGGTTCGCAACACAAAGTGACCCGTAATGATATCTTCCAACTGTTCTCTG
GAGGAATGGGTGGAGAGAGGGTTCACCGACTCCTGAACCGTCATTCCATG
GTAGAGACACTCTAATCTGACTTAACATCGTCAACTTGGTTAAAATTTTC
TTAAATAAATAACTTGTTATTTTAGATGGCTATTTTGTTTGCGTGATTGT
TTTAATAGGGGAATTTTCTTATGTTTAATGAAATGCATACTAAATAATTT
TAAGTCAATAACTAATCATTTAAATGTCTTTAATTATAGTAATGGAACCC
ATTCAAATTCTGCAGAAAGAGCTGGCCCGTGCCCAGCAAGCCAACAAAGC
GCTGTATGAACAAATTATCCAACTCACTCGAGAGATGCATCAAATAAAAA
CCACCTGGGTGGACCCGTCTAAGGTCAAGCCCCTACGCCACAGGCTCACC
GCTGCTCAAAAGGGCTGGGCCGATGAGCAACAAATGAATCAAAACCTTCA
AACACAGATAAGGGGGTTGAAAGTTGCCTTGTCCGCCAGCCAGGAAGGGG
CGGCAGTGACCTACCCTCTTATCTTCGCCCCA
back to top

protein sequence of SMED30013781-orf-1

>SMED30013781-orf-1 ID=SMED30013781-orf-1|Name=SMED30013781-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
MSLIIVMEPIQILQKELARAQQANKALYEQIIQLTREMHQIKTTWVDPSK
VKPLRHRLTAAQKGWADEQQMNQNLQTQIRGLKVALSASQEGAAVTYPLI
FAP
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ