|
| Status |
Public on Sep 11, 2015 |
| Title |
Chrom3-5R-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Chrom3-5R_fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: male
days after eclosion: 5-8
genotype/variation: expressing 5R from Chromosome 3
tissue: Fly Heads
|
| Growth protocol |
Flies were grown on standard medium at 25°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from liquid nitrogen frozen fly heads were extracted with Trizol
libraries were prepared according Zhang et al protocol (PMID: 23273270)
Strand Specific libraries prepared without poly(A) selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
We performed QC using trimmomatic removing PCR primers and low quality bases.
We aligned cleaned read were aligned to the mm10 genome using STAR and selected only for unqiuely mapping reads.
We determined raw reads counts using Bedtools.
Using DESeq, we determined differentially expressed genes.
Genome_build: BDGP6
Supplementary_files_format_and_content: tab delimited text files with raw reads counts per gene
|
| |
|
| Submission date |
Sep 08, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fen-Biao Gao |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Department of Neurology
|
| Street address |
55 Lake Avenue North
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19132 |
| Series (1) |
| GSE72771 |
Differential Toxicity of Nuclear RNA Foci Versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS |
|
| Relations |
| Reanalyzed by |
GSM3276628 |
| BioSample |
SAMN04039298 |
| SRA |
SRX1204201 |
