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Series GSE193091 Query DataSets for GSE193091
Status Public on Jan 05, 2024
Title Maternal inherited siRNA initiate piRNA cluster formation
Organism Drosophila melanogaster
Experiment type Non-coding RNA profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In order to control transposable element (TE) activity, PIWI-interacting RNAs (piRNAs) have been evolved to silence TE transcriptionally and post-transcriptionally, and produced from heterochromatic genomic loci, called piRNA cluster. Maternal inherited piRNAs transmission is considered as the key step of piRNA cluster maintenance and induction of de nove piRNA cluster formation, however, how the original piRNAs were produced without maternal piRNAs deposition remains unclear. In this paper, we created a repetitive GFP reporter and found a Rhino-dependent piRNA cluster conversion spontaneously occurs to the reporter over generations. Importantly, this conversion is reversible by removal of maternal piRNAs of GFP reporter. Taking advantage of this reversible GFP reporter piRNA cluster, we found that siRNA is able to initiate piRNA cluster formation epigenetically, even when only maternal siRNA presence is capable to do so. Our results suggest the importance of siRNA on initiation of piRNA biogenesis and describe a whole picture of initiation and maintenance of piRNA cluster.
 
Overall design Genome occupancy profiling and piRNA production by high throughput sequencing

The submitter noted that
[1] the following processed data files are identical as they contain very few values:

dsGPP_66A6_oxidized_piRNA_1st_S19_R1_001_dsGPP_66A6_oxidized_piRNA_1st_S19_R1_001.dm6.21_22mer.unique.dup.bam.10.mir304_12.Minus.bg4.chopped.bg4
dsGPP_66A6_oxidized_piRNA_2nd_S19_R1_001_dsGPP_66A6_oxidized_piRNA_2nd_S19_R1_001.dm6.21_22mer.unique.dup.bam.10.mir304_12.Minus.bg4.chopped.bg4

dsGPP_66A6_oxidized_piRNA_1st_S19_R1_001_dsGPP_66A6_oxidized_piRNA_1st_S19_R1_001.dm6.21_22mer.unique.dup.bam.10.mir304_12.Plus.bg4.chopped.bg4
dsGPP_66A6_oxidized_piRNA_2nd_S19_R1_001_dsGPP_66A6_oxidized_piRNA_2nd_S19_R1_001.dm6.21_22mer.unique.dup.bam.10.mir304_12.Plus.bg4.chopped.bg4

[2] some samples do not have processed data as only BAM/FASTA files were generated.
 
Contributor(s) Luo Y, He P, Kanrar N, Aravin AA
Citation(s) 37875112
Submission date Jan 05, 2022
Last update date Apr 08, 2024
Contact name Yicheng Luo
E-mail(s) [email protected]
Phone 5167762261
Organization name Calfironia Institute of Technology
Department Division of Biology and Biological Engineering
Street address 1200 E California Blvd
City Pasadena
State/province CA
ZIP/Postal code 91125
Country USA
 
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (104)
GSM5773033 Wild_type_smRNA, rep1
GSM5773034 Wild_type_smRNA, rep2
GSM5773035 20A_plus_single_smRNA, rep1
Relations
BioProject PRJNA794746

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193091_RAW.tar 1.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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