|
| Status |
Public on Jun 17, 2022 |
| Title |
hisrfp_oocyte_rep_D |
| Sample type |
SRA |
| |
|
| Source name |
oocyte
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Stage: late stage oocyte
genotype: w;His2AVRFP(III)
|
| Growth protocol |
standard fly food at 25°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the appropriate time oocytes and embryos were picked into Trizol (Invitrogen #15596026) with 200 ug/ml glycogen (Invitrogen #10814010) and pierced with a 27G needle to release the RNA.
TruSeq RNA sample prep kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw reads were aligned to the BDGP D. melanogaster genome release 6 (dm6) using hisat2 v2.1.0 with the following parameters: -k 2 –very-sensitive (Kim et al., 2015).
Reads aligning to multiple locations were discarded. SAMtools was used to filter (-q 30) and convert file formats (Li et al. 2009).
Reads were assigned to annotated genes using featureCounts v1.5.3 (Liao et al., 2014) using default parameters and the UCSC annotation (r6.20).
The resultant table of read counts was imported into R v4.1.0 and differential expression was determined using DESeq2 v1.33.5. (Love et al., 2014). Genes with < 50 reads across all samples were filtered out.
Differential expression (adjusted p value < 0.05 and fold change > 1) was determined using the standard DESeq2 analysis.
Genome_build: dm6
Supplementary_files_format_and_content: A combined count table of read counts from each file is provided
|
| |
|
| Submission date |
Feb 28, 2022 |
| Last update date |
Jun 17, 2022 |
| Contact name |
Melissa M Harrison |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Wisconsin Madison
|
| Department |
Biomolecular Chemistry
|
| Lab |
1135 Biochemical Sciences Bldg
|
| Street address |
420 Henry Mall
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE197582 |
Precocious expression of Zelda does not initiate early zygotic genome activation |
|
| Relations |
| BioSample |
SAMN26309596 |
| SRA |
SRX14311185 |
