|
| Status |
Public on Dec 31, 2018 |
| Title |
MET.RNASeq Rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Testes
|
| Organism |
Anopheles merus |
| Characteristics |
tissue: Testes
|
| Growth protocol |
All the mosquito stocks were obtained from the Malaria Research and Reference Reagent Resource Center (MR4) in Atlanta (https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Preparation of Illumina libraries The total RNA libraries were prepared in accordance with the Illumina TruSeq RNA sample preparation v2 guide (Part # 15026495, rev.D, September 2012) for Illumina Paired-End Indexed Sequencing. Step 1: RNA purification and fragmentation According to the Illumina mRNA libraries preparation protocol, poly-A mRNA in the tRNA samples were first purified using Illumina poly-T oligo-attached magnetic beads and two rounds of purification. During the second elution of the poly-A-RNA, the mRNA was also fragmented and primed with random hexamers for cDNA synthesis. Step2: Generation of double-stranded cDNA Cleaved mRNAs were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. The RNA template was then removed and a replacement strand synthesized to generate double-stranded cDNA. Step 3: Preparation of ds cDNA samples for Indexed paired-end sequencing Following the standard protocol, after the first and second strand cDNA synthesis, ends were repaired, dA base added, and Illumina indexing adapters were ligated. Finally, cDNA fragments that have adapter molecules on both ends underwent 15 cylcles of PCR to amplify the amount of prepared material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Genome_build:AmerM2.2
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jul 25, 2018 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Richard D Emes |
| E-mail(s) |
richard.emes@nottingham.ac.uk
|
| Phone |
1159516583
|
| Organization name |
University of Nottingham
|
| Department |
School of Veterinary Medicine and Sciences.
|
| Street address |
School of Veterinary Medicine and Science
|
| City |
Nottingham |
| State/province |
Nottinghamshire |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL25378 |
| Series (1) |
| GSE117656 |
Evolution of gene expression levels in Anopheles male reproductive organs |
|
| Relations |
| BioSample |
SAMN09714770 |
| SRA |
SRX4456856 |
