|
Status |
Public on Oct 18, 2016 |
Title |
Tx1Nneg |
Sample type |
SRA |
|
|
Source name |
naive CD31- CD4+ T cell, thymectomy 1
|
Organism |
Homo sapiens |
Characteristics |
cell subtype: naive CD31- CD4+ group: thymectomy 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 |
SAMN04012652 |
SRA |
SRX1164953 |