|
| Status |
Public on Oct 27, 2017 |
| Title |
hypothalamus_heavy_28_1 |
| Sample type |
SRA |
| |
|
| Source name |
hypothalamus_heavy_28
|
| Organism |
Gallus gallus |
| Characteristics |
breed: ROSS308 fast growing-chicken line
day: 42
Sex: male
shear force: heavy
tissue: hypothalamus
replicant: 1
|
| Growth protocol |
The cockerels were reared in a deep-litter facility in experimental farm of the National Research Institute of Animal Production located in Aleksandrowice till 22 or 42 days of age, under the same, optimal, electronically controlled environmental conditions (temperature, lighting regime, air humidity) and were fed ad libitum with the same complete starter (1-21 days of age), grower (22-35 days of age) and finisher (36-42 days of age) diets containing 22, 20.5 and 20.5% crude protein and 2990, 3130 and 3130 kcal/kg metabolic energy.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using PureLink® RNA Mini Kit (Ambion) according to the manufacturer’s protocol. Samples of muscles were homogenised with beads using a Bullet Blender 24 homogenizer (Next Advance). RNA was purified by a bead method (Agencourt RNAClean XP kit) and its quality and quantity was assessed by a Qubit Fluorometer (Invitrogen) and TapeStation 2200 system (RNA tapes, Agilent).
A TruSeq RNA Sample Preparation Kit v2 (Illumina) was used to prepare cDNA libraries from 300 ng aliquots of the RNA samples according to the manufacturer’s protocol. The cDNA samples were ligated with indexed adaptors. Finally, the libraries were amplified in 15 cycles of PCR and their quantity was estimated using the Qubit 2.0 Fluorometer and 2200 TapeStation D1000 tapes. The final concentration of the cDNA libraries was normalised to 10 nM, after which they were pooled .
The libraries were diluted according to a cluster generation protocol and loaded into a v3 Illumina flowcell (16 samples per line with four technical replicates)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
s_4_32pod
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Gallus gallus genome (assembly Gallus_gallus-5.0) with reference annotation containing more than 25K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by Bowtie2 aligner.
Differentially expressed genes and their corresponding p-values were determined using the statistical methods DESeq2
Genome_build: Gallus_gallus-5.0
Supplementary_files_format_and_content: raw.genes.csv.gz: raw genes counts
Supplementary_files_format_and_content: res.pod.csv.gz: DESeq2 results for differential expressed gene analysis of cockerels hypothalamus in different point of life
Supplementary_files_format_and_content: res.prz.csv.gz: DESeq2 results for differential expressed gene analysis of cockerels pituitary in different point of life
|
| |
|
| Submission date |
Sep 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kacper Zukowski |
| E-mail(s) |
zukowski.kacper@gmail.com
|
| Organization name |
National Research Institute of Animal Production
|
| Street address |
Krakowska 1 Street
|
| City |
Balice |
| ZIP/Postal code |
32-083 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21018 |
| Series (1) |
| GSE104255 |
Transcriptomic changes in broiler chicken hypothalamus and pitutary during ontogenesis |
|
| Relations |
| BioSample |
SAMN07702278 |
| SRA |
SRX3216804 |
