|
| Status |
Public on Oct 31, 2019 |
| Title |
WT2_RIP |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovary
strain: Bam-Gal4 :: UASp-GFP
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol™ purification after GFP-trap bead immunoprecipitation.
Libraries were prepared using standard Illumina protocols based on the Illumina TruSeq RNA kit.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
immunoprecipitated RNA
|
| Data processing |
Illumina RTA v2.7.7 was used for basecalling and demultiplexing was performed using Illumina bcl2fastq2-v2.20.0.422
Quality control on the resulting reads was performed with FastQC (v0.11.7). Reads were mapped to the Drosophila genome (FlyBase 6.05) with STAR (v2.4.0). The resulting SAM files were converted to BAM files with SAMtools (v0.1.19)
Sorted BAM files were then used to call counts using Htseq (v0.11.0). Further processing of counts was done using Bioconductor (v3.7) in R (v3.5). Count data was fitted using an inverse beta binomial distribution for paired sample testing in R (Pham et al. (2012). Bioinformatics. i596-i602) for calculating transcript enrichment with respect to control.
Genome_build: Flybase 6.05
Supplementary_files_format_and_content: csv file containing p-values and log(fold changes) arising out of inverse beta binomial algorithm
|
| |
|
| Submission date |
Oct 16, 2019 |
| Last update date |
Oct 31, 2019 |
| Contact name |
Andreas Wodarz |
| E-mail(s) |
andreas.wodarz@uk-koeln.de
|
| Organization name |
Uniklinik Cologne
|
| Department |
Anatomy
|
| Lab |
Molecular Cell Biology
|
| Street address |
Kerpener Str. 62, Building 37
|
| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21306 |
| Series (1) |
| GSE138987 |
Molecular profiling of stem cell-like female germ line cells in Drosophila delineates networks important for stemness and differentiation |
|
| Relations |
| BioSample |
SAMN13041678 |
| SRA |
SRX7007365 |
