|
| Status |
Public on Mar 09, 2016 |
| Title |
BarcodedLibrary18_G_66h_DI |
| Sample type |
SRA |
| |
|
| Source name |
whole tissue
|
| Organism |
Anopheles coluzzii |
| Characteristics |
water type: Freshwater
age post-hatch: 66 hour
exposure time: 6 hours
|
| Treatment protocol |
Exposure for 6 h to either FW or SW
|
| Growth protocol |
Reared in FW until 18 h (or 66 h) post-hatch, at which time experimental exposures (treatment) began
|
| Extracted molecule |
total 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 |
| |
|
| Description |
pool of whole body of 35-50 larvae
|
| Data processing |
Demultiplexing with FASTX-toolkit allowing 1 mismatch, after receipt of fastq files that had been filtered with the Illumina chastity filter
Trimmomatic for trimming adapters and quality filtering (default settings)
mapping reads to An. gambiae PEST genome (AgamP3.7 reference) with Bowtie 2 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 ≥4 libraries), using the R/bioconductor package edgeR
Genome_build: An. gambiae PEST genome (AgamP3.7, downloaded from VectorBase)
Supplementary_files_format_and_content: excel file with counts per million reads of TMM-normalized data for each transcript
|
| |
|
| Submission date |
Jul 21, 2014 |
| 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 |
GPL18984 |
| Series (2) |
| GSE59632 |
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress [set1] |
| GSE74820 |
Transcriptomic differences between euryhaline and stenohaline malaria vector sibling species in response to salinity stress |
|
| Relations |
| BioSample |
SAMN02928792 |
| SRA |
SRX658350 |
