|
| Status |
Public on Jul 13, 2022 |
| Title |
IEC2B |
| Sample type |
SRA |
| |
|
| Source name |
induced endothelial cells, stage day 2
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: induced endothelial cells
time of_differentiation: stage day 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seperated cell samples were treated by Smart-Seq2 protocol to get amplified cDNA.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Useful Perl script was used to filter the original raw data, to trim Smart-seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was finished by Cufflinks 2.2.1.
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 11, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Hai Li |
| E-mail(s) |
lihai@xjtu.edu.cn
|
| Organization name |
Xi'an Jiaotong University
|
| Department |
Department of Pathogenic Microbiology and Immunology
|
| Street address |
No.76 Yanta West Road
|
| City |
Xi'an |
| ZIP/Postal code |
710061 |
| Country |
China |
| |
|
| Platform ID |
GPL19176 |
| Series (1) |
| GSE200624 |
Exploration of the transcriptional regulation network of the differentiation of porcine endothelial cells (ECs) |
|
| Relations |
| BioSample |
SAMN27522136 |
| SRA |
SRX14817496 |
