|
| Status |
Public on Jul 31, 2020 |
| Title |
CD4-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B-NDG
tissue: Spleen
cell type: T cells
cell subtype: CD4
|
| Treatment protocol |
1000 T cells were sorted for RNAseq analysis.
|
| Growth protocol |
The process cells derived from ESC/iPSC.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The procedure of RNA extraction and reverse transcription into double-stranded DNA were prepared using Discover-sc WTA Kit V2(Vazyme, N711)
Libraries were prepared according to instruction of TruePrepTM DNA Library Prep Kit V2 (Vazyme,TD503).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bcl2fastq convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2. And the used samtools to convert and sort the sam file to bam file. StringTie were used to calculated genes expression level in TPM.
Gene expression levels of different samples were normalized by Stringtie, and finally generated TPM table with R
Genome_build: mm10
Supplementary_files_format_and_content: TPM table was a csv file
|
| |
|
| Submission date |
Oct 17, 2018 |
| Last update date |
Jul 31, 2020 |
| Contact name |
Jinyong Wang |
| E-mail(s) |
wang_jinyong@gibh.ac.cn
|
| Organization name |
Guangzhou Institutes of Biomedicine and Health (GIBH)
|
| Street address |
190 Kai Yuan Avenue, Science Park, Guangzhou, China
|
| City |
Guangzhou |
| State/province |
GuangDong |
| ZIP/Postal code |
510530 |
| Country |
China |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE121373 |
T cell regeneration from pluripotent stem cells by defined transcription factors [T cells [CD4 and CD8]) |
| GSE121375 |
T cell regeneration from pluripotent stem cells by defined transcription factors |
|
| Relations |
| BioSample |
SAMN10250653 |
| SRA |
SRX4896775 |
