|
| Status |
Public on Mar 02, 2021 |
| Title |
hyp-40: low growth rate, hypothalamus |
| Sample type |
SRA |
| |
|
| Source name |
Kołudzka White Geese
|
| Organism |
Anser anser |
| Characteristics |
day: 108
Sex: male
growth rate: low
replicant: 4
tissue: hypothalamus
|
| Growth protocol |
Sixty 1-day-old male strain W33 of White Kołuda® geese were individually weighed and randomly allocated in 4 pens of 15 birds each on deep litter. During the first 4 weeks of the rearing birds were kept indoors, under controlled temperature and humidity environment and then, up to week 15.5 they had access to free range. All birds were kept in semi-intensive rearing system according to the oat-fattening technology
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by RNA was isolated by the PureLink™ RNA Mini Kit (Ambion, Cambridge, UK) according to the manufacturer’s recommendations. The RIN values were over 7 what was estimated by TapeStation2200 and RNA tapes (Agilent, Palo Alto, USA).
The cDNA libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
The de novo alignment using Trinity
Annotation and counting using Blast/Kallisto/Salmon
Genome_build: GCA_002592135.1
Genome_build: GCA_002166845.1
Supplementary_files_format_and_content: raw.genes.ab.csv.gz: compressed gzip file containing raw genes counts for GCA_002592135.1
Supplementary_files_format_and_content: raw.genes.ac.csv.gz: compressed gzip file containing raw genes counts for GCA_002166845.1
Supplementary_files_format_and_content: raw.genes.ad.kallisto.csv.gz: compressed gzip file containing raw genes counts for de novo experiment and kallisto
Supplementary_files_format_and_content: raw.genes.ad.salmon.csv.gz: compressed gzip file containing raw genes counts for de novo experiment and salmon
Supplementary_files_format_and_content: results.genes.ab.hypothalamus.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002592135.1
Supplementary_files_format_and_content: results.genes.ab.pituitary.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002592135.1
Supplementary_files_format_and_content: results.genes.ac.hypothalamus.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002166845.1
Supplementary_files_format_and_content: results.genes.ac.pituitary.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002166845.1
Supplementary_files_format_and_content: results.genes.ad.kallisto.hypothalamus.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo kallisto experiment and hypothalamus
Supplementary_files_format_and_content: results.genes.ad.kallisto.pituitary.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo kallisto experiment and pituitary
Supplementary_files_format_and_content: results.genes.ad.salmon.hypothalamus.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo salmon experiment and hypothalamus
Supplementary_files_format_and_content: results.genes.ad.salmon.pituitary.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo salmon experiment and pituitary
|
| |
|
| Submission date |
Mar 01, 2021 |
| Last update date |
Mar 02, 2021 |
| 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 |
GPL29787 |
| Series (1) |
| GSE167941 |
Hypothalamic -pituitary axis changes related to growth rate in Kołudzka White geese |
|
| Relations |
| BioSample |
SAMN18093767 |
| SRA |
SRX10194342 |
