SMED30034813

Overview
NameSMED30034813
Smed IDSMED30034813
Length (bp)881
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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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Alignments
SMED30034813 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013940:6319..7172 -2910
Homology
BLAST of SMED30034813 vs. Planmine SMEST
Match: SMESG000025382.1 (SMESG000025382.1)

HSP 1 Score: 203.756 bits (517), Expect = 4.769e-66
Identity = 99/106 (93.40%), Postives = 101/106 (95.28%), Query Frame = -2
Query:  212 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVSNSTPLATPSTVPSSNY 529
            NKALYEQIIQLTKEVQQVK TWVDPAKLKSIHQRLT AQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDS S+STPL TPS VPS+NY
Sbjct:   25 NKALYEQIIQLTKEVQQVKFTWVDPAKLKSIHQRLTAAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSASSSTPLTTPSAVPSNNY 130          
BLAST of SMED30034813 vs. Planmine SMEST
Match: SMESG000006905.1 (SMESG000006905.1)

HSP 1 Score: 196.823 bits (499), Expect = 2.227e-63
Identity = 96/106 (90.57%), Postives = 101/106 (95.28%), Query Frame = -2
Query:  212 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVSNSTPLATPSTVPSSNY 529
            NK+LYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPS LAYR+S +NST   TPST+PSSN+
Sbjct:   18 NKSLYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSLLAYRNSANNSTFAVTPSTIPSSNH 123          
BLAST of SMED30034813 vs. Planmine SMEST
Match: SMESG000065111.1 (SMESG000065111.1)

HSP 1 Score: 196.052 bits (497), Expect = 4.094e-63
Identity = 94/106 (88.68%), Postives = 100/106 (94.34%), Query Frame = -2
Query:  212 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVSNSTPLATPSTVPSSNY 529
            NK+LYEQI+QLTKEVQQVKSTWVDPAKLKSIHQRLT AQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQ+AYRDS++NST    PS VPSSN+
Sbjct:   18 NKSLYEQILQLTKEVQQVKSTWVDPAKLKSIHQRLTAAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQVAYRDSINNSTLAVNPSAVPSSNH 123          
BLAST of SMED30034813 vs. Planmine SMEST
Match: SMESG000021386.1 (SMESG000021386.1)

HSP 1 Score: 196.438 bits (498), Expect = 5.658e-63
Identity = 95/106 (89.62%), Postives = 100/106 (94.34%), Query Frame = -2
Query:  212 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVSNSTPLATPSTVPSSNY 529
            NKALYEQIIQLTKEVQQVKSTWV+P KLKSIHQ LT AQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDS ++STPL TPS +PS+NY
Sbjct:   18 NKALYEQIIQLTKEVQQVKSTWVNPTKLKSIHQSLTAAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSANSSTPLVTPSAIPSNNY 123          
BLAST of SMED30034813 vs. Planmine SMEST
Match: SMESG000072856.1 (SMESG000072856.1)

HSP 1 Score: 192.2 bits (487), Expect = 1.313e-61
Identity = 92/106 (86.79%), Postives = 100/106 (94.34%), Query Frame = -2
Query:  212 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVSNSTPLATPSTVPSSNY 529
            NK LYEQIIQLTKEVQQVKSTWVDPAKLK +HQRLT AQKGWAEE+QLNQNL  QI+GLEVALAASREGEAVTYPLIFAPSQLAYRDSV+N TP+ATPST+PS++Y
Sbjct:   18 NKVLYEQIIQLTKEVQQVKSTWVDPAKLKPLHQRLTAAQKGWAEEQQLNQNLLAQIKGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSY 123          
The following BLAST results are available for this feature:
BLAST of SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 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 SMED30034813 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025382.14.769e-6693.40SMESG000025382.1[more]
SMESG000006905.12.227e-6390.57SMESG000006905.1[more]
SMESG000065111.14.094e-6388.68SMESG000065111.1[more]
SMESG000021386.15.658e-6389.62SMESG000021386.1[more]
SMESG000072856.11.313e-6186.79SMESG000072856.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034813 ID=SMED30034813|Name=SMED30034813|organism=Schmidtea mediterranea sexual|type=transcript|length=881bp
AATTCAATGTTATTTATTTTTTACAACGTACCACTTTTAAATAATTTAGC
AATAATTACAATTTTACATTCAATTCATATAACAATAAAAACGATTAAAT
TAGACAATATTTGTAAGTGAGTTCAATGTCAAAGCGATACACGACACATT
AAGTTAATTTATTTGCCAGGCGTGCGGCTCTGCGTCGGGTGCGTTCTTTA
CGTCCCGGCCGGTAATTGCTTGAAGGGACCGTCGATGGAGTCGCTAATGG
CGTTGAGTTGCTGACAGAATCCCGGTATGCCAATTGAGATGGGGCGAAGA
TAAGAGGGTAAGTCACCGCTTCTCCTTCACGACTGGCGGCCAAGGCGACT
TCCAACCCCCTTATCTGCGTCCGGAGGTTCTGATTTAGTTGGCGTTCCTC
AGCCCAACCCTTTTGAGCAGTTGTGAGACGTTGGTGGATGGACTTGAGTT
TTGCTGGGTCCACCCAGGTGGATTTCACCTGCTGTACCTCCTTTGTGAGC
TGAATTATCTGCTCGTATAGAGCTTTGTTGGATTGCTGGGCGCGGGATAA
TTCCTGTTGTAGTAATTGGGCCAGTTCCATGGCTAATAGAAAATAATAAT
TTAAGGGGAGAGGTTTGCTGATAGGGCGGAATCATATAATTTATATTTAA
TCCAAACAAACTATTGAAAATAACTAAAACTCTAAACTAATCAAAAACAA
AACACAAAAATTATTTTTAATTAACATTAATCAAACTAATCAAAACAAAA
AGGAGGACAATTAGTCCTAACTATCATTGATCAAATTTGAGTCTTTGTCT
GCTCAGAGAAAGCCTTTCGCCACCCATTCCTCGGGTGTATAGCCCGAGAT
CGACCTGGTCGGTCTCTTTGTGTTGCGGGCT
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protein sequence of SMED30034813-orf-1

>SMED30034813-orf-1 ID=SMED30034813-orf-1|Name=SMED30034813-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
MELAQLLQQELSRAQQSNKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQ
RLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQL
AYRDSVSNSTPLATPSTVPSSNYRPGRKERTRRRAARLANKLT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ