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| Status |
Public on May 31, 2021 |
| Title |
RNA het 20ApD_42ABD ovaries rep1 |
| Sample type |
SRA |
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| Source name |
ovaries
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
tissue: ovaries
age: adult
genotype: 20A(p)-delta/+; 42AB-delta/+
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from dissected adult ovaries was isolated using Trizol reagent (Invitrogen) and quantified using Qubit (Invitrogen). Contaminating DNA was removed using RQ1 DNAse as described by the manufacturer (Promega).
Poly(A)-selected RNA-sequencing (RNA-seq) analysis was performed on 2.5µg of total RNA using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina®.
Libraries were multiplexed using the NEBNext® Multiplex Oligos for Illumina® and sequenced in single-end, 50-nt-long reads on an Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Poly(A)-selected RNA
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| Data processing |
RNA-seq data were mapped to the Drosophila melanogaster genome (dm3) and the FlyBase and Repbase transposon consensus database using the piPipes package (version 1.5.0; https://github.com/bowhan/piPipes), following the RNA-seq pipeline (Han et al., 2015).
Libraries were aligned to ribosomal RNA using Bowtie2 (Langmead and Salzberg, 2012), and non-rRNA-mapping reads were then mapped to the transcriptome and transposon consensus using Bowtie2.
dm3
bigwig files generated using the piPipes package
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| Submission date |
May 17, 2021 |
| Last update date |
May 31, 2021 |
| Contact name |
Daniel Gebert |
| E-mail(s) |
[email protected]
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| Organization name |
University of Cambridge
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| Department |
Department of Genetics
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| Lab |
Felipe Karam Teixeira
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| Street address |
Downing Street
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| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 3EH |
| Country |
United Kingdom |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE174561 |
Large Drosophila Germline piRNA Clusters are Evolutionarily Labile and Dispensable for Transposon Regulation |
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| Relations |
| BioSample |
SAMN19233515 |
| SRA |
SRX10912822 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5319667_Het_20ApD_42ABD_rep1.dm3.sorted.uni.minus.bigWig |
26.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM5319667_Het_20ApD_42ABD_rep1.dm3.sorted.uni.plus.bigWig |
25.6 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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