 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 12, 2020 |
| Title |
A524 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Bos taurus |
| Characteristics |
breed: Red Angus
Sex: female
cell type: leukocytes
condition: heat stress
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was collected from tail veins of healthy cattle and anticoagulated with EDTA. Blood samples (5 ml) were centrifuged at 3000 × g for 15 min at 4 °C and white coat (leukocytes) was transferred to a new 2-ml cryopreservation tube to which 1 ml RNAiso Plus (Takara, Dalian, China) was added before snap freezing in liquid nitrogen for transport. Total RNA was extracted with RNAiso Plus (Takara) according to manufacturer protocols.
All mRNA-Seq libraries were sequenced on an Illumina Novaseq platform (San Diego, CA) following the manufacturer’s protocol. Quantity and purity of RNA and RNA-Seq libraries were determined by Beijing Novogene Bioinformatics Technology (Beijing, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Index of the B. taurus reference genome ARS-UCD1.2 was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.16.1).
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: readcount_18.txt: Tab-delimited text file includes read count values for each Sample.
Supplementary_files_format_and_content: novel_genes.txt: Tab-delimited text file.
|
| |
|
| Submission date |
Jun 04, 2020 |
| Last update date |
Jun 12, 2020 |
| Contact name |
Gongwei zhang |
| E-mail(s) |
zhanggongwei@swu.edu.cn
|
| Phone |
+08617723574530
|
| Organization name |
西南大学
|
| Street address |
重庆市荣昌区学院路160号
|
| City |
重庆 |
| ZIP/Postal code |
402460 |
| Country |
China |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE151817 |
Inheritance Patterns of Leukocyte Gene Expression Under Heat Stress in F1 Hybrids Cattle and Their Parents |
|
| Relations |
| BioSample |
SAMN15102257 |
| SRA |
SRX8472340 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
