|
| Status |
Public on Jun 30, 2016 |
| Title |
W1118_3 |
| Sample type |
SRA |
| |
|
| Source name |
Abdomen fly extracts enriched in fat body content
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: Four-six day old flies
genotype: Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Qiagen RNeasy Mini Kit
The polyA fraction was purified using two rounds of oligo dT-magnetic bead purification. The resulting polyA fraction was fragmented and first strand cDNA was done with random primers. The resulting first strand cDNA was purified using AMPure Beads and second strand cDNA and end repair was done using standard techniques. The blunt ended double stranded cDNA was incubated with exo- E.coli DNA polymerase to add an adenosine to the ends for T/A cloning of the adaptors. A second round of PCR amplification was done to add unique 6-bp barcodes to each sample and add sequences necessary for flow cell attachment. The resulting mRNA libraries were quantitated using qPCR following the manufacturer's instructions (Kapa Biosystems, Woburn MA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads were mapped to UCSC dm3 using TopHat v2.0.10 guided by dm3 GTF from UCSC with default parameters.
Underlying Bowtie2 v2.1.0 was used within the TopHat tool.
Transcript abundances were calculated using Cufflinks v2.1.1 (Cufflinks -> Cuffmerge -> Cuffdiff) with default parameters.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text output file from Cuffdiff which includes FPKM values for both Samples.
|
| |
|
| Submission date |
Mar 17, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria De Luca |
| E-mail(s) |
mdeluca2@uab.edu
|
| Phone |
2059347033
|
| Organization name |
UAB
|
| Street address |
Webb 451 - 1720 Second Ave. South
|
| City |
Birmingham |
| State/province |
Alabama |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL17275 |
| Series (1) |
| GSE67001 |
RNA-sequencing of abdominal fat body-enriched tissue of Drosophila fat body-specific Sdc RNAi knockdown and control |
|
| Relations |
| Reanalyzed by |
GSM3287783 |
| BioSample |
SAMN03421313 |
| SRA |
SRX957956 |
