|
| Status |
Public on Aug 09, 2012 |
| Title |
HS_VQ (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
whole individuals
|
| Organism |
Harpegnathos saltator |
| Characteristics |
tissue: whole body
sample type: virgin queen
|
| Treatment protocol |
total RNA is extracted by TRIzol Reagent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 ug total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3'overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using Illumina HiSeq 2000 and the paired-end sequencing module.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sequenced reads were generated from whole individuals of Harpegnathos saltator virgin queens after removal of gut and poison glands.
|
| Data processing |
RNA-Seq reads were aligned onto the corresponding v3.5 reference genomes using TopHat v1.0.12 with default parameters.
|
| |
|
| Submission date |
Aug 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Hong zhi Cao |
| E-mail(s) |
caohongzhi@genomics.cn
|
| Phone |
8675525274032
|
| Organization name |
BGI-SHENZHEN
|
| Department |
Bioinformatics
|
| Street address |
F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518083 |
| Country |
China |
| |
|
| Platform ID |
GPL14138 |
| Series (2) |
| GSE31346 |
Transcriptome sequencing of queen and virgin queen of two ants: Camponotus floridanus and Harpegnathos saltator |
| GSE31577 |
Genome-wide analysis of global and caste-specific DNA methylation in two ant species: Camponotus floridanus and Harpegnathos saltator |
|
| Relations |
| SRA |
SRX091811 |
| BioSample |
SAMN00709351 |
