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| Status |
Public on Jan 15, 2014 |
| Title |
Dmel_F_BR2_TR2 |
| Sample type |
SRA |
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| Source name |
Adult Head Tissue
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| Organism |
Drosophila melanogaster |
| Characteristics |
biological replicate: BR2
technical replicate: TR2
Sex: female
developmental stage: adult
strain: Berlin (BDSC 8522)
tissue: head
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| Growth protocol |
Flies were raised on standard food medium at 25C on a 12 hour light dark cycle.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Invitrogen).
Solexa/Illumina libraries were constructed according to manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Primer and adapter sequences were trimmed using custom perl scripts.
Each sample was first evaluated with TopHat to create a set of read-supported junctions.
Reads were aligned to D. melanogaster genome FB (FlyBase v5) using Bowtie ( --best, --tryhard, --paired end). Reads aligning more than 10 times were removed from consideration.
Unaligned reads were then unpaired and realigned using Bowtie.
Remaining unaligned reads were mapped to the junctions from TopHat.
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM), Average Number of Reads Per Nucleotide (APN).
Genome_build: Flybase 5
Supplementary_files_format_and_content: Are in the CSV format. With the following columns: common contig id, number of reads in the common region, total mappable reads, length of the common region in bp, RPKM. See Series supplementary file for location of contig on the genome.
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| Submission date |
Jan 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lauren McIntyre |
| E-mail(s) |
mcintyre@ufl.edu
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| Organization name |
University of Florida
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL11203 |
| Series (2) |
| GSE54067 |
RNA-seq: technical variability and sampling (female) |
| GSE54069 |
RNA-seq: technical variability and sampling |
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| Relations |
| Reanalyzed by |
GSM3285180 |
| BioSample |
SAMN02584312 |
| SRA |
SRX426464 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1306661_dmel_female_22_common_contig_rpkm.csv.gz |
303.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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