|
| Status |
Public on Oct 14, 2015 |
| Title |
high shear force 3 |
| Sample type |
SRA |
| |
|
| Source name |
high shear force of pectoralis musle
|
| Organism |
Gallus gallus |
| Characteristics |
strain: Hubbard Flex
gender: female
age: 6 week
sample group: high shear force
tissue: pectoralis muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pectoralis muscle were stabilized by RNAlater solution and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 300 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Cleaned sequences were aligned to the Gallus gallus genome (Galgal 4.74 assembly) with a reference annotation containing 17,954 genes listed in the Ensembl database.
The alignment and estimation of gene and isoforms level expression was made using TopHat and RSEM package, both supported by a Bowtie2 aligner.
The differential expression estimation was proceed with utilization of cuffdiff, edgeR and DeSeq2 Bioconductor R-project packages.
Genome_build: galGal4 (Gallus_gallus-4.0; http://www.ncbi.nlm.nih.gov/assembly/GCF_000002315.3)
Supplementary_files_format_and_content: output files from cuffdiff, edgeR and DeSeq2 Bioconductor R-project packages;
raw*.csv.gz containing raw genes or isoforms counts
cuffdiff.*exp.diff.gz containing TopHat results for differential expression analysis (high vs low) for genes or isoforms
edgeR.DeSeq2.results*.csv.gz containing egred and DeSeq2 results for differential expression analysis (high vs low) for genes or isoforms
|
| |
|
| Submission date |
Oct 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Katarzyna Piorkowska |
| E-mail(s) |
katarzyna.piorkowska@izoo.krakow.pl
|
| Organization name |
National Research Institute of Animal Production
|
| Department |
Animal Genomics and Molecular Biology
|
| Lab |
Laboratory of Genomics
|
| Street address |
Krakowska 1
|
| City |
Balice |
| ZIP/Postal code |
32-083 |
| Country |
Poland |
| |
|
| Platform ID |
GPL21018 |
| Series (1) |
| GSE73940 |
Genome-wide RNA-Seq analysis of breast muscles of two broiler chicken groups differing in shear force |
|
| Relations |
| BioSample |
SAMN04122841 |
| SRA |
SRX1302967 |
