SMED30002275

Overview
NameSMED30002275
Smed IDSMED30002275
Length (bp)434
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.
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
Anatomical Expression

PAGE et. al., 2020



SMED30002275

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30002275h1SMcG0003267 SmedASXL_012755SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X1 cellSMED30002275h1SMcG0003267 SmedASXL_004094SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30002275h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002275h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30002275h1SMcG0003267 dd_Smed_v4_74366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002275h1SMcG0003267 dd_Smed_v4_74366_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30002275h1SMcG0003267 dd_Smed_v4_29867_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30002275h1SMcG0003267 dd_Smed_v4_21908_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
Alignments
SMED30002275 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001669:110243..110676 -2170
v31.005754:283..716 -2152
Homology
[Close]
BLAST of SMED30002275 vs. Planmine SMEST
Match: SMESG000018097.1 (SMESG000018097.1)

HSP 1 Score: 281.567 bits (719), Expect = 1.702e-88
Identity = 144/144 (100.00%), Postives = 144/144 (100.00%), Query Frame = 3 
Query:    3 SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI 434
            SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI
Sbjct:  336 SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI 479
[Close]
BLAST of SMED30002275 vs. Planmine SMEST
Match: SMESG000018097.1 (SMESG000018097.1)

HSP 1 Score: 280.796 bits (717), Expect = 1.951e-88
Identity = 144/144 (100.00%), Postives = 144/144 (100.00%), Query Frame = 3 
Query:    3 SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI 434
            SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI
Sbjct:   83 SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESSQIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDDEDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI 226
The following BLAST results are available for this feature:
BLAST of SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 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 SMED30002275 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000018097.11.702e-88100.00SMESG000018097.1[more]
SMESG000018097.11.951e-88100.00SMESG000018097.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002275 ID=SMED30002275|Name=SMED30002275|organism=Schmidtea mediterranea sexual|type=transcript|length=434bp
CTTCTAAAAAAATTTCTTTATTTCAAGATATCTCTAAACAGCTATATTTT
ATTTATAAAGAAATTTTAGATTTTAATCGCAAATTCGGCGATGAAATTTA
TTGTTCAACTTTAGACAAATTTCAAACGGGCAACATTTATGATGAATCCA
GTCAAATAATCATTGTCTTTCTGAAGCTAATAAATTACATATCCTTATCT
ATAGAAAATTACGAAATAAATAATTTAAAATATGATAAAAACAGCGAGAT
AAAGCCATCAATGTATATATTCCTTGATTCAGTAGACTTATTGTGCGATG
ATGAAGACATGACAGTGGTGGGAAACTTTGTCATTAATTTCCCATTACGT
GTTAGAATCATTTTAACTATCTCAAATCTAACTATATTGGATGAATCAAA
AATCATAAACATTCCAAAACTGGAGTCAAACATC
back to top

protein sequence of SMED30002275-orf-1

>SMED30002275-orf-1 ID=SMED30002275-orf-1|Name=SMED30002275-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
SKKISLFQDISKQLYFIYKEILDFNRKFGDEIYCSTLDKFQTGNIYDESS
QIIIVFLKLINYISLSIENYEINNLKYDKNSEIKPSMYIFLDSVDLLCDD
EDMTVVGNFVINFPLRVRIILTISNLTILDESKIINIPKLESNI
back to top