|
| Status |
Public on Mar 09, 2024 |
| Title |
shNC1 |
| Sample type |
SRA |
| |
|
| Source name |
porcine induced pluripotent stem cells
|
| Organism |
Sus scrofa |
| Characteristics |
development stage: 26.5d
breed: Bamei black pig
cell type: induced pluripotent stem cells
genotype: Negative Control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1.Total RNA was extracted using RNAiso Plus reagent; 2.mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA; 3.RNA fragmentation and cDNA synthesis; 4.End repair, add A and adaptor ligation; 5.PCR; 6.Circularization and make DNB.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
BGIseq500 platform used for basecalling.
Align clean reads to the reference genes by using Bowtie2 to get the alignment result
The sequencing data was filtered with SOAPnuke (v1.5.2).
The expression level of gene was calculated by RSEM (v1.2.12).
Genome_build: GCF_000003025.6_Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM values for every gene and every sample
|
| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
Mar 09, 2024 |
| Contact name |
Wu Xiaolong |
| E-mail(s) |
2018050593@nwafu.edu.cn
|
| Organization name |
Northwest A&F University
|
| Department |
College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering and Technology
|
| Street address |
College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering and Techn
|
| City |
yangling |
| State/province |
Shannxi |
| ZIP/Postal code |
712100 |
| Country |
China |
| |
|
| Platform ID |
GPL26285 |
| Series (1) |
| GSE168591 |
LIN28A inhibited DUSP family phosphatases and activated MAPK signaling pathway to maintain pluripotency in porcine induced pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN18235188 |
| SRA |
SRX10298349 |
