|
| Status |
Public on Jun 23, 2017 |
| Title |
CORO1A_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila whole head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: whole head
Sex: female
tissue-specific knockdown: neuronal
RNAi driver: elav-GAL4>Dicer2
human knockdown gene: CORO1A
fly knockdown gene: coro
fly knockdown vdrc line: 44672
|
| Growth protocol |
Flies were reared with elav-Gal4>Dicer2 driver at 25°C on conventional cornmeal-sucrose-dextrose-yeast medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
F1 female progeny were collected in groups of 40-50, quickly frozen in liquid nitrogen, and stored at −80°C. For RNA extraction, the heads were separated from their bodies by repetitive cycles of freezing in liquid nitrogen and vortexing. Total RNA was isolated using TRIZOL (Invitrogen, Carlsbad, CA).
We prepared cDNA libraries using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Trimmomatic (Bolger et al., 2014) was first used to trim reads as necessary, based on FastQC (bioinformatics.babraham.ac.uk/projects/fastqc) output.
TopHat2 v.2.1.0 (Kim et al., 2013) was used to align the raw sequencing data to the reference fly genome and transcriptome.
HTSeq-Count v.0.6.1 (Anders et al., 2015) was used to calculate raw read counts for each gene.
Genome_build: Dmel 6.08
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts for all transcripts (three technical replicates per biological sample in each file).
|
| |
|
| Submission date |
Jun 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Santhosh Girirajan |
| E-mail(s) |
sxg47@psu.edu
|
| Phone |
814-865-0674
|
| Organization name |
Pennsylvania State University
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
205A Life Sciences Building
|
| City |
State College |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE100387 |
Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster |
|
| Relations |
| Reanalyzed by |
GSM3283710 |
| BioSample |
SAMN07269744 |
| SRA |
SRX2947716 |
