|
| Status |
Public on Aug 10, 2017 |
| Title |
Control injection - rep2 |
| Sample type |
SRA |
| |
|
| Source name |
brain (minus optic lobes)
|
| Organism |
Harpegnathos saltator |
| Characteristics |
treatment: control
|
| Treatment protocol |
On the 6th day of transition, ants that had been dueling for three consecutive days were transferred to a new nest in groups of 6. Three were injected with synthetic corazonin and three with a controlled scrambled peptide. Each ant was injected with a calibrated glass capillary needle directly into the head, right behind the antennas, or into the gaster with 100 ng of peptide dissolved in 0.5 ml of ant saline.
|
| Growth protocol |
Animals were housed in a plaster nest in a clean, temperature (25°C) and humidity (50%) controlled ant facility on a 12-hour light/dark cycle and fed three times per week with live crickets.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Brains (minus optic lobes) were dissected and RNA extracted with TRIzol. DNA was removed using Turbo DNAse.
RNA was fragmented by boiling in presence of divalent cations. RT was performed with random hexamers and dUTP was incorporated in the 2nd strand to retain strand information.
Strand-specific RNA-seq (dUTP)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
control.injection.d1.b2
submitter provided internal id: raw_data/FASTQ/2015/151031_NS500234_0147_AHFG7YBGXX/151031.HFG7YBGXX.ND64.R2.gz
|
| Data processing |
Reads were aligned to Hsal v3.0 & OGS3.5 with STAR (version 2.5.0b)
Counts were assigned to gene models in Hsal OGS3.8 using the R package DEG-seq
RPKMs were calculated by only considering reads assigned to protein-coding genes
Differential expression was determined with the R package DESeq2 including all sequenced samples in the experiment for variance stabilization
Assembly and annotation were described in Bonasio et al. Science 2010 (PMID: 20798317) and Bonasio et al. Current Biol 2012 (PMID: 22885060). Assembly and annotations can be downloaded from the Hymenoptera Genome Database, using the following links.
Genome_build: http://hymenopteragenome.org/harpegnathos/?q=genome_consortium_datasets
Genome_build: Hsal v3.0
Supplementary_files_format_and_content: Table of raw RNA-seq counts and normalized RPKM values for all genes models in OGS3.8
Supplementary_files_format_and_content: Output table from DESeq2 including maximum a posteriori log-fold-change, raw P-values, and adjusted P-values
|
| |
|
| Submission date |
Jun 28, 2016 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL22089 |
| Series (2) |
| GSE83806 |
Brain RNA-seq one day intra-head injection of corazonin or control peptide in Harpegnathos ants. |
| GSE83807 |
Caste-specific gene expression in ants |
|
| Relations |
| BioSample |
SAMN05301059 |
| SRA |
SRX1883148 |
