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Sample GSM3092496 Query DataSets for GSM3092496
Status Public on Aug 09, 2018
Title piwi-sKD (C2GnS1)
Sample type SRA
 
Source name Drosophila 0-2 h embryos
Organism Drosophila melanogaster
Characteristics genotype: w ; tj-GAL4 ; tubP-GAL80[ts] sh-piwi
tissue: Drosophila 0-2 h embryos
temperature: 25°C
Growth protocol [no-KD] Flies were grown at 20°C
[piwi-sKD] Flies were grown at 20°C exept in the last 5 days (25°C)
Extracted molecule other
Extraction protocol DNA was extracted from 0-2 h embryos using the DNeasy Blood & Tissue Kit (Qiagen) and further purified with the PCR purification kit (Qiagen). Linear genomic DNA was digested with Plasmid-Safe™ ATP-Dependent DNase (Lucigen) and the remaining eccDNA molecules were then amplified by rolling circle amplification (RCA) using Illustra TempliPhi kit (GE Healthcare) and random primers.
The libraries were prepared with Nextera XT library kit (Illumina).
250 nucleotides paired-end sequencing was performed on a MiSeq platform (Illumina) by Plateau de Génotypage CIRAD (France).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
 
Description extra chromosomal circular DNA (eccDNA)
S8_S7_L001
Data processing Mobilome reads were mapped with Bowtie2 version 2.2.4 (using parameters -k 10 -N 1) on the Drosophila melanogaster genome (dm3) complemented with canonical TE sequences.
TE annotated reads were re-mapped again using canonical TEs as references, with Bowtie2 version 2.2.4 (using parameters -k 10 -N 1), to attribute each read to a TE family.
Our full analysis pipeline is available at https://bitbucket.org/blaiseli/pirna-pipeline /mobilome.
Genome_build: Drosophila melanogaster genome (dm3)
Supplementary_files_format_and_content: .txt files with read counts for TEmapping reads for each analysed TE in different mapping categories (F=sense read, R= antisense read, mm=mismatch) (#ref = TE-family, total = sense and antisense reads with up to 4 mismatches, total_F = all sense reads, total_R = all antisense reads , F_0mm = sense reads with 0 mismatches , R_0mm = antisense reads with 0 mismatches , F_mm = sense reads with 1 ore more mismatches, R_mm = antisense reads with 1 ore more mismatches, F_1_mm = sense reads with 1 mismatch, R_1_mm = antisense reads with 1 mismatch, F_2_mm = sense reads with 2 mismatches, R_2_mm = antisense reads with 2 mismatches, F_3_mm = sense reads with 3 mismatches, R_3_mm = antisense reads with 3 mismatches) for each sequenced condition.
 
Submission date Apr 11, 2018
Last update date Aug 09, 2018
Contact name SEVERINE CHAMBEYRON
E-mail(s) [email protected]
Organization name CNRS
Department Institute of Human Genetics
Lab Non-coding RNA, epigenetics and genome stability
Street address 141, rue de la Cardonille
City MONTPELLIER
ZIP/Postal code 34396
Country France
 
Platform ID GPL16479
Series (2)
GSE112968 Somatic piRNA pathway prevents transgenerational germline transposition [circularDNA-seq]
GSE112972 Somatic piRNA pathway prevents transgenerational germline transposition
Relations
BioSample SAMN08915457
SRA SRX3923507

Supplementary file Size Download File type/resource
GSM3092496_C2Gn_embryons_TE_on_TE_ref_counts.txt.gz 2.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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