|
| Status |
Public on Jul 31, 2022 |
| Title |
Intestine_ind1 |
| Sample type |
SRA |
| |
|
| Source name |
individual 1_Intestine
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Leghorn
individual id: individual 1
age: 12-mo
Sex: male
tissue: Intestine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen tissues using Macherey-Nagel Nucleo-Spin® RNA kit according to the manufacturer’s instructions and mRNA were selected using poly-T beads
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA sample prep kit
RNA-seq experiments (paired-end read length of 2x150 pb) have been performed on an Illumina NovaSeq 6000 with the Illumina NovaSeq 6000 sequencing kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
control quality with FastQC software
alignment with STAR software (version 2.604a) on annotated exons
counting with featureCounts software (version 1.6.3)
differentially expressed gene analysis using SARTools-DESeq2 R package (Varet et al, 2016, PloS one, 11(6):e0157022)
Genome_build: Genome Reference Consortium Chicken Build 6a/GCA 00002315.5 (https://www.ncbi.nlm.nih.gov/genome/111?genome_assembly_id=451987)
Supplementary_files_format_and_content: featureCounts matrix table
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Sophie Fouchécourt |
| E-mail(s) |
sophie.fouchecourt@inra.fr
|
| Organization name |
INRA
|
| Lab |
PRC
|
| Street address |
Centre Val de Loire
|
| City |
NOUZILLY |
| State/province |
FRANCE |
| ZIP/Postal code |
37380 |
| Country |
France |
| |
|
| Platform ID |
GPL26853 |
| Series (1) |
| GSE133401 |
Transcriptome of eight rooster (Leghorn) tissues for identification of differentially expressed genes |
|
| Relations |
| BioSample |
SAMN12147527 |
| SRA |
SRX6370063 |
