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GEO Series: GSE63228

Title: Xenopus Piwi protein associated transcripts indicate regulation beyond transposons

Summary

This study examines the population of transcripts associated with the Xenopus Piwi proteins, Xiwi and Xili, from X.laevis and X.tropicalis. RIP-seq, CLIP-seq, piRNA-seq, and mRNA-seq datasets were integrated to determine how the Xenopus Piwi proteins where using piRNAs and binding interactions to associate with transcripts in gonadal cells.


Contributors: Nelson Lau, Trey Toombs, Yuliya Sytnkova, Gungwei Chirn, Michael Blower

Experiment Type: We performed several replicates of a Piw CLIP-Seq experiment to isolate RNA fragments as CLIP-tags to discover which transcripts are preferentially bound by the Piwi protein. Then we performed several types of mRNA expression profiling experiments using several forms of mRNA-Seq library construction formats. Finally, we sequenced the piRNAs from the OSS cells

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
oocyte - oocyte III-IV GSM1544074  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte oocyte stage III to oocyte stage IV  
oocyte - oocyte V-VI GSM1544075  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte oocyte stage V to oocyte stage VI  
piwil1 oocyte - adult GSM1544071  GSM1544072  CLIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil1 Ab2
piwil1 spermatid - adult GSM1544073  CLIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
spermatid adult frog stage piwil1 Ab2
piwil2 oocyte - adult GSM1544070  CLIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil2 Ab1
oocyte - adult GSM1544080  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage  
piwil1 oocyte - adult GSM1544078  RIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil1 Ab2
piwil1 oocyte - adult GSM1544076  ncRNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil1 Ab2
piwil2 oocyte - adult GSM1544079  RIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil2 Ab1
piwil2 oocyte - adult GSM1544077  ncRNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte adult frog stage piwil2 Ab1
Select All 
Xtr   
Xla 

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