|
| Status |
Public on Jun 26, 2022 |
| Title |
RRBS_F1C_APH_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
APH
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Cobb
age: 10
treatment: paternal non-conditioned
tissue: APH
|
| Treatment protocol |
Hatched chicks were weighed, their sex was identified according to wing feathering, and they were tagged and randomly divided into 8 chicks per pen in climate-controlled rooms at 32°C under a 22/2 h cycle of artificial illumination with ad libitum access to food and water. On day 7 posthatch, the temperature was changed to 30°C and chicks were further divided into 5 chicks per pen.
|
| Growth protocol |
We used 80 fertile Cobb strain broiler (Gallus gallus) eggs from one breeder flock of hens. The eggs were randomly divided into two incubation treatments: CTRL – eggs were incubated at 37.8°C and 56% relative humidity throughout the 21 days of the incubation period; EHC – eggs were incubated at 39.5°C and 65% relative humidity for 12 h/day on embryonic days 7 to 16
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated by TRI Reagent.
Libraries were prepared using Zymo-Seq RRBS Library Kit (Zymo).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Trimming of Illumina adapters, as well as quality trimming, were performed with Trim Galore
Reads were mapped to the chick genome (galGal5.0) using Bismark v. 0-22-3, bowtie mode. Next, methylation calls were extracted with Bismark, methylation extractor mode.
Differential methylation on a single CpGs site (DMS) was extracted and analyzed by edgeR, with the recommended cutoff of at least 8 reads in every sample before being considered in the analysis and FDR < 0.05. DMRs were extracted and analyzed by metilene v. 0.2-8.
Genome_build: galGal5_0
Supplementary_files_format_and_content: Bedgraph files were generated using Bismark
|
| |
|
| Submission date |
Oct 28, 2021 |
| Last update date |
Jun 26, 2022 |
| Contact name |
Tali Rosenberg |
| E-mail(s) |
tzabaryt@gmail.com
|
| Phone |
0524403600
|
| Organization name |
ARO
|
| Street address |
Hamacabim
|
| City |
Rishon Lezion |
| ZIP/Postal code |
7692000 |
| Country |
Israel |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE186742 |
Embryonic heat conditioning in chicks induces transgenerational heat/immunological resilience via methylation on regulatory elements |
|
| Relations |
| BioSample |
SAMN22635791 |
| SRA |
SRX12810813 |
