|
| Status |
Public on Dec 31, 2021 |
| Title |
DPLG4KO15 |
| Sample type |
SRA |
| |
|
| Source name |
ovaries
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: mutant for the gene DPLG4
tissue: ovary
|
| Growth protocol |
All flies were maintained at 25 degree centigrade in standard Drophila melanogaster media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Direct-zol kit (Zymo Research) and stored at -70°C.
RNA was sent to Genomics Core Facility at Cornell University for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQC program was used to determine that all raw data passed quality control test to be used for downstream analyses.
STAR aligner (version 2.5) was used to map the RNA-Seq reads to the D. melanogaster reference genome (genome assembly BDGP6.88).
HTseq was used for counting reads.
DESeq2 was used for differential expression analyses with a FDR of 5%.
For analyzing differential transposable (TE) element expression, STAR aligner was used to map the RNA-Seq reads to the D. melanogaster reference genome with an additional flag --outFilterMultimapNmax 100 and TEtranscripts followed by DESeq2 was used for differential expression of TEs with FDR of 5%.
Genome_build: GRCh37
Supplementary_files_format_and_content: Files with raw gene counts for every gene
|
| |
|
| Submission date |
Dec 08, 2020 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Diwash Jangam |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Texas at Arlington
|
| Department |
Biology
|
| Lab |
Betran lab
|
| Street address |
701 S. Nedderman Drive
|
| City |
Arlington |
| State/province |
TX |
| ZIP/Postal code |
76019 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE162866 |
PIF transposases are recurrently domesticated as ovary and nervous system regulatory proteins in Drosophila |
|
| Relations |
| BioSample |
SAMN17028916 |
| SRA |
SRX9651762 |
