|
| Status |
Public on Nov 01, 2017 |
| Title |
brain_gl60j_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
W3L_brain_gl60j
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: brain
sample type: D.mel. W3L brain gl60j 25C
|
| Treatment protocol |
Dissected in 0.1M Phosphate Buffer
|
| Growth protocol |
Grown on molasses food at 25C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol, DNase treatment, RNeasy clean-up, Sodium Acetate precipitation
Illumina TruSeq RNA v2 sample preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
D.mel. W3L brain gl60j 25C
|
| Data processing |
sequencing adapters and low quality bases were removed with Trimmomatic v0.33 with paramaters TruSeq3-PE-2.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20
trimmed reads were aligned to the Drosophila reference genome dm3 with Tophate v2.2.1 using default parameters
gene expression was calculated from aligned reads with Cufflinks v2.2.1 with default parameters using the RefSeq genome annotation for Drosophila genome build dm3
Differential gene expression was computed between genotypes with the Cufflinks/cuffdiff protocol v2.2.1
Genome_build: Drosophila melanogaster dm3
Supplementary_files_format_and_content: processed data is provided in an Excel spreadsheet with gene expression values normalized as FPKM valules by Cufflinks v2.2.1
|
| |
|
| Submission date |
May 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Carolyn Morrison |
| E-mail(s) |
[email protected]
|
| Phone |
212-263-1031
|
| Organization name |
NYU School of Medicine
|
| Department |
Skirball Institute
|
| Lab |
Treisman
|
| Street address |
540 First Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
11746 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE99303 |
Glass promotes the differentiation of both neuronal and non-neuronal cells in the Drosophila eye |
|
| Relations |
| BioSample |
SAMN07168175 |
| SRA |
SRX2857462 |
