|
| Status |
Public on May 24, 2018 |
| Title |
H. sal embryo - whole body - rep2 |
| Sample type |
SRA |
| |
|
| Source name |
H. sal embryo_whole body
|
| Organism |
Harpegnathos saltator |
| Characteristics |
developmental stage: embryo
tissue: whole body
|
| 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 |
RNA was extracted from full bodies 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 |
HS.embryo.b2
internal reference: 160205.HL72VBGXX.ND85.R1.gz
|
| Data processing |
reads were aligned to Hsal v8.5 with STAR (version 2.5.0b). 75 bp were clipped from the 3' end to produce 125 bp reads, and max intron length was set to 10,000 bp.
counts were assigned to gene models in Hsal OGS4.0 or Hsal lncRNA4.0 using the R package DEG-seq
RPKMs were calculated by DEG-seq
Differential expression was determined with the R package DESeq2 using variance stabilization models.
Genome_build: Hsal v8.5
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS4.0 and Hsal lncRNA4.0
|
| |
|
| Submission date |
Aug 14, 2017 |
| 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) |
| GSE102604 |
Whole body RNA-seq from developmental stages of Harpegnathos ants |
| GSE102605 |
RNA-seq from Camponotus and Harpegnathos ants for genome annotation |
|
| Relations |
| BioSample |
SAMN07503284 |
| SRA |
SRX3091742 |
