|
| Status |
Public on Sep 01, 2013 |
| Title |
3 day old heads spermidine food 1 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
food: standard Drosophila media with 5mM spermidine
age: 3 days after eclosion
tissue: heads
|
| Treatment protocol |
Flies were cultured either in the presence or absence of 5mM spermidine
|
| Growth protocol |
Flies were cultures according to standard methods at 25 degrees with a 12 hour light dark cycle
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Spd- and Spd+ flies were frozen in liquid nitrogen and heads were collected after vortexing by mechanical separation. Poly A+ RNA was extracted from approximately 50 ul of heads per sample using the RNeasy Lipid tissue Mini kit (Qiagen) and the Oligotex mRNA mini kit (Quiagen). RNA was reverse transcribed into a cDNA using the Superscript III Reverse Transcriptase Kit (Invitrogen) for first strand synthesis. Second strand synthesis was performed with E.coli and T4 DNA polymerases (New England Biolabs). DNA end repair was performed on 9-20 ng of cDNA followed by ligation of adaptors, and size selection for 300 bp fragments using the E-gel Size Select gel (Invitrogen). Fragments were amplified using 14 PCR cycles and linear amplification was validated by qPCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Raw data was processed using the default Illumina CASAVA pipeline, with mapping to the dm3 genome using ELAND with 0 or 1 mismatches.
Normalized expression values were generated using the Genomatix Genome Analyser v2. 40901.
Genome_build: BDGP R5 / dm3
Supplementary_files_format_and_content: bed files contain one line for each mapped read; wig files are standard
|
| |
|
| Submission date |
Jul 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jamie M Kramer |
| E-mail(s) |
j.kramer@gen.umcn.nl
|
| Organization name |
Radboud University Nijmegen Medical Centre
|
| Street address |
Geert Grootplein 10
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11203 |
| Series (1) |
| GSE38998 |
RNA sequencing in fly heads to examine the effect of spermidine feeding on transcription in the ageing fly brain. |
|
| Relations |
| Reanalyzed by |
GSM3284268 |
| BioSample |
SAMN02251431 |
| SRA |
SRX323032 |
