|
| Status |
Public on Aug 01, 2020 |
| Title |
Mammary gland cells, Blank-2 |
| Sample type |
SRA |
| |
|
| Source name |
Blank-2_goatmg
|
| Organism |
Capra hircus |
| Characteristics |
breed: Lanshan dairy goat
cell type: mammary gland cells cultured in 3D condition
treatment: Blank
genotype: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
goat mammary gland cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Processed data file : AllSamples.GeneExpression.FPKM.txt
The group information is prefixed with Blank_2 in the column of processed data file
|
| Data processing |
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of -m 0 -x 1000 -s 40 -l 35 -v 3 -r 2. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR 0.001 and an absolute value of log2Ratio1 to judge the significance of gene expression difference.
Genome_build: ARS1
Supplementary_files_format_and_content: FPKMs
|
| |
|
| Submission date |
Aug 11, 2019 |
| Last update date |
Aug 01, 2020 |
| Contact name |
Yong Zhao |
| E-mail(s) |
[email protected]
|
| Phone |
86-18661613617
|
| Organization name |
Qingdao Agricultural University
|
| Department |
College of Life Sciences
|
| Lab |
B604
|
| Street address |
700 Changcheng Road
|
| City |
Qingdao |
| State/province |
Shandong |
| ZIP/Postal code |
266109 |
| Country |
China |
| |
|
| Platform ID |
GPL15473 |
| Series (1) |
| GSE135692 |
RNA-seq of goat mammary gland cells samples from different treatment groups |
|
| Relations |
| BioSample |
SAMN12558324 |
| SRA |
SRX6696968 |
