|
| Status |
Public on Mar 09, 2016 |
| Title |
M-20-RC |
| Sample type |
SRA |
| |
|
| Source name |
An. merus_20%_6 hrs_whole tissue
|
| Organism |
Anopheles merus |
| Characteristics |
water salinity (%): 20
age: 18 h post-hatch
exposure time: 6 hours
tissue: pool of whole body of 35-50 larvae
|
| Treatment protocol |
Exposure for 6 h to either water of one of the following salinities: 0, 10, 20, 30, 40, or 50 percent the salinity of sea water
|
| Growth protocol |
Reared in FW until 18 h post-hatch, at which time experimental exposures (treatment) began
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted and DNAse treated
TruSeq® RNA Sample Preparation kit v2 (Illumina) for construction of RNA libraries (including a polyA-selection step), following manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Demultiplexing and filtering with the Illumina chastity filter
Trimmomatic for trimming adapters and quality filtering (default settings)
mapping reads to An. gambiae PEST genome (AgamP4.2 reference) with Bowtie2 and TopHat2
HTSeq (union option) to count numbers of uniquely mapped reads
TMM normalization, and exclusion of reads with low counts (<1 count per million reads in ≥3 libraries), using the R/bioconductor package edgeR; exclusion of reads mapped to rRNA
Genome_build: An. gambiae PEST genome (AgamP4.2, downloaded from VectorBase; https://www.vectorbase.org/)
Supplementary_files_format_and_content: counts per million reads of TMM-normalized data for each transcript
|
| |
|
| Submission date |
Nov 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hilary April Uyhelji |
| Organization name |
University of Notre Dame
|
| Department |
Biological Sciences
|
| Street address |
317 Galvin Life Science Center
|
| City |
Notre Dame |
| State/province |
IN |
| ZIP/Postal code |
46556 |
| Country |
USA |
| |
|
| Platform ID |
GPL18985 |
| Series (2) |
| GSE74819 |
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set2] |
| GSE74820 |
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress |
|
| Relations |
| BioSample |
SAMN04252518 |
| SRA |
SRX1424941 |
