|
| Status |
Public on May 24, 2018 |
| Title |
C. flo instar 1 larvae - whole body - rep2 |
| Sample type |
SRA |
| |
|
| Source name |
C. flo instar 1 larvae_whole body
|
| Organism |
Camponotus floridanus |
| Characteristics |
developmental stage: instar 1 larva
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 twice weekly with excess supplies of water, 20% sugar water (sucrose cane sugar), and Bhatkar-Whitcomb diet.
|
| 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 |
CF.inst1.b2
internal reference: 160205.HL72VBGXX.b1202.R1.gz
|
| Data processing |
reads were aligned to C. flo v7.4 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 Cflo OGS4.0 or Cflo 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: Cflo v7.4
Supplementary_files_format_and_content: Table of normalized RPKM values for all genes models in OGS4.0 and Cflo 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 |
GPL20286 |
| Series (2) |
| GSE102603 |
Whole body RNA-seq from developmental stages of Camponotus ants |
| GSE102605 |
RNA-seq from Camponotus and Harpegnathos ants for genome annotation |
|
| Relations |
| BioSample |
SAMN07503299 |
| SRA |
SRX3091729 |
