|
| Status |
Public on Jun 26, 2022 |
| Title |
RNA-seq t0 Non-Cond parents rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Anterior preoptic hypothalamus
|
| Organism |
Gallus gallus |
| Characteristics |
cell type: whole tissue lysate
treatment: t0 Non-Cond parents
age: day 10 posthatch
|
| Treatment protocol |
Nonconditioned F1 chicks (day 10 posthatch) were subjected to Heat challenge (moved from 30°C environment to 36°C environment) or LPS Challenge (LPS was injected into the third ventricle). Chicks were sacrificed 6 hours into each challenge and their APH dissected. Unchallenged groups (t0) were used as controls. mRNA WAS extracted using Tri-Reagent. Total RNA was isolated from each sample and subjected to RNA-Seq.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriReagent.
15 ng of purified RNA was used for library preparation with the bulk MARS-seq method (Jaitin et al. 2014 Science.343:776-9).100bp single reads were sequenced on a Novaseq 6000 sequencing system. The output was ~25 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
t0_F1C_2
|
| Data processing |
Poly-A/T stretches and Illumina adapters were trimmed from the reads using Cutadapt. Resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome (galGal5.0, UCSD) according to Refseq annotations, using STAR.Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Read counts per gene were calculated using HTSeq-count, with the following parameters: 'htseq-count -s no --mode=union’. Normalization and differential expression analysis were performed using the DESeq2. Differentially expressed genes (DEG) were defined as genes that had a significant adjusted p value (padj) of less than 0.05 and at least 2-fold change. To elucidate gene alterations across all analyzed groups, the expression of all DEG was assessed. Respective heat maps were generated by custom R scripts and the Complexheatmap R package.
Assembly: galGal5
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 17, 2022 |
| 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 |
SAMN28494948 |
| SRA |
SRX15312116 |
