|
| Status |
Public on Oct 28, 2020 |
| Title |
miRNA-TC3 |
| Sample type |
SRA |
| |
|
| Source name |
Chorioallantoic membrane (CAM) of embryos
|
| Organism |
Gallus gallus |
| Characteristics |
embryo: Chorioallantoic membrane
age: 11-day of embryo
genotype: Tibetan chicken
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Chorioallantoic membrane tissues were removed, frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit (Cat.#RS-122-2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Hiseq used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then aligned to the chicken reference genome (Gallus gallus 6.0) using HISAT2 (version 2.0.9) software
FPKM and TPM were calculated using the StringTie, Differential expression analysis comparing TC and CH was performed with the DESeq2 software.
Genome_build: Gallus-gallus-6.0 (ftp://ftp.ensembl.org/pub/release-96/fasta/gallus_gallus/dna)
Supplementary_files_format_and_content: bam profiles
|
| |
|
| Submission date |
Oct 28, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Ying Zhang |
| E-mail(s) |
zhangsiwu444@126.com
|
| Organization name |
China Agricultural University
|
| Street address |
Haidian District, Yuanmingyuan West Road 2
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL23499 |
| Series (1) |
| GSE160324 |
Comprehensive analysis of coding and non-Coding RNA transcriptomes related to hypoxic adaptation in the Tibetan chickens |
|
| Relations |
| BioSample |
SAMN16582146 |
| SRA |
SRX9390124 |
