|
| Status |
Public on Jan 02, 2014 |
| Title |
CS mRNA |
| Sample type |
SRA |
| |
|
| Source name |
Whole insect- adult Musca domestica; strain CS
|
| Organism |
Musca domestica |
| Characteristics |
strain: CS
|
| Growth protocol |
M. domestica were reared at 27C (12:12 L:D) on a diet of Calf manna, Brewer's yeast, powdered skim milk, wheat bran, and sugar.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to Illumina's instructions accompanying the mRNA Seq 8-sample kit by the Hudson Alpha Institute of Biotechnology, Huntsville, AL. Libraries were then sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Insecticide susceptible strain for additional comparison
|
| Data processing |
Differential expression: The reference transcriptome was generated de novo using Trinity. Contigs were then compressed using CAP3 and the resulting contigs and singletons files were then annotated for coding regions using the Fly model in Augustus. Gene annotation was then conducted using HMM Scan against the PFam database (version 26.0) and Blastx homology to Drosophila melanogaster (version r5.44) using BLOSUM64 and an e-value cut off of 10-10. The coding trimmed sequences from Augustus were then used as the mapping reference for the individual FASTQ files from each strain. trace reads were mapped using RSEM to generate FPKM estimates. Gene expression levels were compared to the ALHF strain using EdgeR.
Genome_build: NCBI_TSA#KA644422-KA650580
Supplementary_files_format_and_content: FPKM expression comparison
|
| |
|
| Submission date |
Jul 13, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nannan Liu |
| E-mail(s) |
liunann@auburn.edu
|
| Phone |
334-844-2661
|
| Fax |
334-844-5005
|
| URL |
http://www.ag.auburn.edu/enpl/faculty/liu.htm
|
| Organization name |
Auburn University
|
| Department |
Entomology
|
| Lab |
Liu
|
| Street address |
301 Funchess Hall
|
| City |
Auburn |
| State/province |
AL |
| ZIP/Postal code |
36849 |
| Country |
USA |
| |
|
| Platform ID |
GPL15805 |
| Series (1) |
| GSE39327 |
A Whole Transcriptional Linkage Analysis of Gene Co-Regulation in Insecticide Resistant House Flies, Musca domestica |
|
| Relations |
| SRA |
SRX159764 |
| BioSample |
SAMN01087795 |
