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Status |
Public on Aug 09, 2018 |
Title |
piwi-sKD (C2GnS1) |
Sample type |
SRA |
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Source name |
Drosophila 0-2 h embryos
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Organism |
Drosophila melanogaster |
Characteristics |
genotype: w ; tj-GAL4 ; tubP-GAL80[ts] sh-piwi tissue: Drosophila 0-2 h embryos temperature: 25°C
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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)
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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).
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina MiSeq |
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Description |
extra chromosomal circular DNA (eccDNA) S8_S7_L001
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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.
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Submission date |
Apr 11, 2018 |
Last update date |
Aug 09, 2018 |
Contact name |
SEVERINE CHAMBEYRON |
E-mail(s) |
[email protected]
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Organization name |
CNRS
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Department |
Institute of Human Genetics
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Lab |
Non-coding RNA, epigenetics and genome stability
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Street address |
141, rue de la Cardonille
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City |
MONTPELLIER |
ZIP/Postal code |
34396 |
Country |
France |
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Platform ID |
GPL16479 |
Series (2) |
GSE112968 |
Somatic piRNA pathway prevents transgenerational germline transposition [circularDNA-seq] |
GSE112972 |
Somatic piRNA pathway prevents transgenerational germline transposition |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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