|
| Status |
Public on Jun 22, 2019 |
| Title |
SG n=2 |
| Sample type |
SRA |
| |
|
| Source name |
Salivary glands
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: y1 w67c23
tissue: Salivary glands
cell cycle: endoreplication
|
| Growth protocol |
Flies were kept at 25ºC. After introducing males and females for 2 days, females were allowed to lay eggs for 6 hours and flipped to a new vial. Four days after egg lay, feeding 3rd instar larvae were taken from the food and BD and SG were dissected out.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol (ThermoFisher, cat# 15596026).
Libraries were generated according TruSeq Stranded mRNA Library Prep kit (Illumina, cat#20020594) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
GSF1939-SG-n-2_S4_R1_001.fastq
Poly-A tail enriched RNA
|
| Data processing |
Read quality analyzed with FastQC (0.11.5).
Reads mapped to Dmel R6.23 whole genome using STAR (2.6.1a) with special parameters: --outSAMtype BAM SortedByCoordinate
Aligned reads assigned to features from the Dmel R6.23 GTF annotation file using the R (3.3.1) bioconductor (3.3) Rsubread (1.24.2) featureCounts function using the special parameters: isGTFAnnotationFile=T, strandSpecific=2.
Differential expression of the raw feature counts from Rsubread performed using the R (3.3.1) bioconductor (3.3) DESeq2 (1.14.1) DESeq function with default parameters.
Genome_build: Dmel R6.23
Supplementary_files_format_and_content: Excel raw feature counts, fold-change
|
| |
|
| Submission date |
Oct 30, 2018 |
| Last update date |
Jun 22, 2019 |
| Contact name |
Brian R Calvi |
| E-mail(s) |
[email protected]
|
| Phone |
812-855-5450
|
| Organization name |
Indiana University Bloomington
|
| Department |
Biology
|
| Lab |
Calvi
|
| Street address |
1001 E. 3rd St.
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE121956 |
RNAseq on developmental endoreplicating (salivary glands) cells in Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN10348647 |
| SRA |
SRX4957334 |
