|
| Status |
Public on Oct 18, 2016 |
| Title |
HC2MEMneg |
| Sample type |
SRA |
| |
|
| Source name |
memory (CD45RA-) CD4 T cell, healthy control 2
|
| Organism |
Homo sapiens |
| Characteristics |
cell subtype: memory (CD45RA-) CD4
group: healthy control
cell type: T cells (FACSsorted)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from sorted CD31+ and CD31- naïve CD4+ T cells using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) as according to manufacturer’s instructions. RNA was stored at -80C until further processing
mRNA was isolated using the Poly(A) Beads (NEXTflex). Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI37) using BWA package ( mem –t 7 –c 100 –M –R ).
The RPKM values and the raw read numbers were calculated using the rnaseq_countgeneread function from Cisgenome v2
Genome_build: hg19
Supplementary_files_format_and_content: *.rna raw read counts
Supplementary_files_format_and_content: *.rna.RPKM RPKM values
|
| |
|
| Submission date |
Aug 26, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Michal Mokry |
| E-mail(s) |
m.mokry@umcutrecht.nl
|
| Organization name |
Wilhelmina Children's Hospital, University Medical Center Utrecht
|
| Street address |
Lundlaan 6
|
| City |
Utrecht |
| ZIP/Postal code |
3584 EA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE72400 |
naive T cell heterogeneity after neonatal thymectomy |
|
| Relations |
| BioSample |
SAMN04012645 |
| SRA |
SRX1164946 |
