|
| Status |
Public on Oct 31, 2019 |
| Title |
Bam3 |
| Sample type |
SRA |
| |
|
| Source name |
ovary
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovary
strain: vas-GFP; bam_delta86/bam_delta86
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol™ purification from single-cell suspensions of GFP+ FACS-sorted cells of respective genotypes.
Libraries were prepared using standard Illumina protocols based on the Illumina TruSeq RNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava v1.8.2 was used for basecalling
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 used to call counts using Htseq (v0.11.0). Further processing of counts was done using Bioconductor (v3.7) in R (v3.5). Counts were normalized and differential expression was calculated using DESeq2 (v1.14.0).
Genome_build: Flybase 6.05
Supplementary_files_format_and_content: normalization parameters arising out of DESeq2
|
| |
|
| 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 |
GPL13304 |
| Series (1) |
| GSE138987 |
Molecular profiling of stem cell-like female germ line cells in Drosophila delineates networks important for stemness and differentiation |
|
| Relations |
| BioSample |
SAMN13041686 |
| SRA |
SRX7007357 |
