|
| Status |
Public on Mar 07, 2019 |
| Title |
Growth period of calcification in high strength group [HSG-3] |
| Sample type |
SRA |
| |
|
| Source name |
laying hen
|
| Organism |
Gallus gallus |
| Characteristics |
breed: Hy-Line Brown
tissue: Uterus
age: 42 weeks
eggshell strength group: high strength
egg calcification period: Growth
|
| Treatment protocol |
The uterine samples were taken from the laying hens which laying hard and weak-shell eggs during calcification periods respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Trizol Reagent, after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit(Illumina, USA).
First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
HSG-3
HSGvsLSG.DEG.fasta; HSGvsLSG.html
|
| Data processing |
The corresponding sequence reads were mapped to the chicken genome in Ensembl using Bowtie2/Tophat2 (http://tophat.cbcb.umd.edu).
Genes with ׀fold change׀> 1.5 and padj < 0.05 were identified as DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the functions of DEGs.
Genome_build: Galgal4 (GCA_000002315.2)
Supplementary_files_format_and_content: raw_counts.txt
Supplementary_files_format_and_content: nomalized_counts.txt
Supplementary_files_format_and_content: fasta: Differential expression genes.
Supplementary_files_format_and_content: html: KEGG path
|
| |
|
| Submission date |
Mar 06, 2019 |
| Last update date |
Mar 08, 2019 |
| Contact name |
Desheng Qi |
| E-mail(s) |
zjc404@webmail.hzau.edu.cn
|
| Phone |
15972103964
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Animal Nutrition and Feed Science
|
| Street address |
Shizishan Street No.1
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL10223 |
| Series (1) |
| GSE127974 |
Uterine transcriptome of hens laying hard or weak-shell eggs |
|
| Relations |
| BioSample |
SAMN11080006 |
| SRA |
SRX5488011 |
