 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 31, 2021 |
| Title |
DNA w1118 female flies |
| Sample type |
SRA |
| |
|
| Source name |
whole flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
tissue: whole body
age: adult
genotype: control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was obtained from 20-40 female adult flies from w1118 and a triple mutant (20A(p)∆; 38C∆, 42AB∆) stock. DNA was extracted using the Quick-DNA Microprep Kit w/ Zymo-Spin™ (Zymo Research) and quantified using Qubit (Invitrogen).
Library preparation was performed on 0.25µg of genomic DNA using the Nextera DNA Flex Library Prep kit as described by the manufacturer (Illumina).
Libraries were multiplexed and sequenced in paired-end, 150-nt-long reads on an Illumina NovaSeq.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Paired-end reads were mapped to the D. melanogaster genome using BWA MEM (Li and Durbin, 2009).
The resulting SAM/BAM files were then filtered to retain only uniquely mapping reads using Samtools (Li et al., 2009) and the command line utility grep. A map quality filter with a threshold value of 60 was applied with Samtools.
Bigwig files were created with Bedtools (Quinlan and Hall, 2010) and the UCSC genome browser command-line tool bedGraphToBigWig.
Analysis of total genomic TE copy numbers was conducted by mapping paired-end reads to the complete set of D. melanogaster TE consensus sequences (FlyBase) using bowtie2 and limiting the number of distinct valid alignments to one per read (‘-k 1’). Read counts for each TE family were were multiplied by 150 nt paired-end read base pairs (300), divided by TE consensus sequence length and genomic read coverage.
dm3
bigwig files generated by BWA MEM, samtools, bedtools and bedGraphToBigWig
|
| |
|
| Submission date |
May 17, 2021 |
| Last update date |
May 31, 2021 |
| Contact name |
Daniel Gebert |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Cambridge
|
| Department |
Department of Genetics
|
| Lab |
Felipe Karam Teixeira
|
| Street address |
Downing Street
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 3EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25244 |
| Series (1) |
| GSE174561 |
Large Drosophila Germline piRNA Clusters are Evolutionarily Labile and Dispensable for Transposon Regulation |
|
| Relations |
| BioSample |
SAMN19233507 |
| SRA |
SRX10912808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5319653_w1118.bwa.uniq.bigwig |
234.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
