 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 24, 2013 |
| Title |
Pupae |
| Sample type |
SRA |
| |
|
| Source name |
Pupae
|
| Organism |
Bactrocera dorsalis |
| Characteristics |
life stage: Pupae
|
| Treatment protocol |
none
|
| Growth protocol |
Liquid Artificial Diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen Rneasy Plus Mini Kit
Illumina TruSeq RNA Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Transcriptome assembly using Trinity r2012_10_05 using all reads, in silico normalized to ~30x coverage
Alignment of concatenated reads to assembly using Bowtie 0.12.7
Abundance estimation on alignment file using RSEM 1.2.0
Filtering assembly based on RSEM TPM cutoff = 0.5, IsoPct cutoff = 5 and presence of likely coding region
Aligning individual samples to filtered assembly using Bowtie 0.12.7, abundance estimation with RSEM 1.2.0
Raw read count files from RSEM were TMM normalized and FPKM transformed to produce normailzed abundance measurements
Genome_build: n/a
Supplementary_files_format_and_content: Files are tab-separated text files containing either read or TMM normalized FPKM values for each developmental stage at a gene and isoform (transcript) level
|
| |
|
| Submission date |
Apr 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Hall |
| Organization name |
USDA PBARC
|
| Street address |
64 NOWELO ST
|
| City |
Hilo |
| State/province |
Hawai'i |
| ZIP/Postal code |
96720 |
| Country |
USA |
| |
|
| Platform ID |
GPL17054 |
| Series (1) |
| GSE46310 |
Bactrocera dorsalis Gene expression |
|
| Relations |
| BioSample |
SAMN02055464 |
| SRA |
SRX261509 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
