|
| Status |
Public on Mar 30, 2017 |
| Title |
bam_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bam
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: bam
gender: male
age: 3 days old
tissue: adult testes
|
| Growth protocol |
The flies were kept at 23°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
50 adult testes were dissected in PBS. Total RNA was isolated from testes, using TRIZol (Invitrogen) reagent, according to the manufacturer’s instructions.
One microgram of total RNA was processed for library preparation using the RNA TruSeq kit. The libraries were sequenced on the Illumina MiSeq system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Bam_vs_WT_CuffDiff_Output_BDGP5.txt
|
| Data processing |
Reads were aligned on D.melanogaster BDGP R5/dm3 (or BDGP R6/dm6) genome assembly (https://genome-euro.ucsc.edu/) using TopHat (–r 200 –mate-std-dev 50) .
Transcript differential expression testing between samples was performed with Cuffdiff using geometric normalization, pooled dispersion estimation and FDR 0.05
Transcript assembly was performed by Cufflinks (BDGP R6/dm6).
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: gene abundance and log2(fold_change)
|
| |
|
| Submission date |
Mar 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Petr Laktionov |
| E-mail(s) |
laktionov@mcb.nsc.ru
|
| Organization name |
Institute of molecular and cellular biology SD RAS
|
| Lab |
Genomics lab
|
| Street address |
Lavrenitev ave 8/2
|
| City |
Novosibirsk |
| ZIP/Postal code |
630090 |
| Country |
Russia |
| |
|
| Platform ID |
GPL16479 |
| Series (2) |
| GSE97129 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis [RNA-Seq] |
| GSE97182 |
Genome-wide profiling of gene expression and transcription factors binding reveals new insights into the mechanisms of gene regulation during Drosophila spermatogenesis |
|
| Relations |
| Reanalyzed by |
GSM3283159 |
| BioSample |
SAMN06651304 |
| SRA |
SRX2683539 |
