|
| Status |
Public on Apr 13, 2020 |
| Title |
Testosterone replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
8 pooled ovarian germinal discs
|
| Organism |
Gallus gallus |
| Characteristics |
breed: White Leghorn
Sex: Female
tissue: ovarian germinal discs
drug treatment: Testosterone (1.5mg in 0.5ml peanut oil)
time collected before ovulation: 3.5 hours
replicate: 1
|
| Treatment protocol |
Treatment & tissue collection protocol: White leghorn laying hens (Gallus gallus) were injected with either corticosterone (1.5mg dissolved in 0.5ml peanut oil), testosterone (1.5mg dissolved in 0.5ml peanut oil), or a control injection (0.5ml peanut oil) at 5h prior to predicted ovulation based on previous laying patterns. All hens were killed via lethal injection approximately 1.5h post-injection (which is 3.5h before ovulation), when the sex chromosomes should be segregating, and the F1 follicles were collected. The GD region was removed from the F1 follicle and briefly washed in Krebs buffer to remove any yolk material. It was placed in 0.5mL reaction tube filled with 100μl of Buffer RL (Norgen Biotek Corp.). Then 100μl of 70% ethanol was added to the sample and it was vortexed thoroughly until the GD material was completely broken down. The samples were placed in -80°C for future use.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation protocol: The RNA from the samples was extracted using the Norgen’s Single Cell RNA Purification Kit (catalog no. 51800, Norgen Biotek Corp.). A Nanodrop© spectrophotometer (ND-1000 Nanodrop Technologies, Wilmington, DE, USA) was used to assess the initial RNA purity and concentration of each sample. To ensure adequate RNA quantity for analysis, we pooled nine GD region samples (8μl from each) per replicate. We created 5 pooled replicates per treatment group, for a total of 15 replicates. The RNA integrity of each replicate was assessed on an Agilent 2100 Bioanalyzer instrument (Model 62939B, Agilent Technologies, Santa Clara, CA, USA) at the Georgia Genomics and Bioinformatics Core (GGBC) at the University of Georgia (Athens, GA).
RNA-Seq for the Illumina' TruSeq strand-specific kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TEST1
processed data file: Ggal_RNA_Seq_raw_count_matrix.txt
|
| Data processing |
Read mapping was performed using TopHat v2.0.14.
Raw count extraction was performed using HTSEQ v0.6.1p1.
Genome_build: Ensembl: ftp://ftp.ensembl.org/pub/release-93/fasta/gallus_gallus/dna/Gallus_gallus.Gallus_gallus-5.0.dna.toplevel.fa.gz
Supplementary_files_format_and_content: Ggal_RNA_Seq_raw_count_matrix.txt: Tab-delimited text file, raw count matrix.
|
| |
|
| Submission date |
May 16, 2019 |
| Last update date |
Apr 13, 2020 |
| Contact name |
Kristen Jean Navara |
| E-mail(s) |
knavara@gmail.com
|
| Phone |
7065421369
|
| Organization name |
The University of Georgia
|
| Department |
Poultry Science
|
| Street address |
203 Poultry Science Building
|
| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (1) |
| GSE131363 |
The effects of testosterone and corticosterone treatment on gene expression in germinal discs of the laying hen |
|
| Relations |
| BioSample |
SAMN11664039 |
| SRA |
SRX5850019 |
