|
| Status |
Public on Sep 15, 2015 |
| Title |
HC_C_min |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Healthy control
tissue: Peripheral Blood
cell type: CD4+CD45RO+ T cells
treatment: JQ1(-)
|
| Treatment protocol |
Cells were cultured for 16h in the presence of 300 nM JQ1(+) or JQ1(-). Next, cells were treated for 4h with 100 ng/mL phorbol 12-myristate 13-acetate and 1 µg/mL ionomycin.
|
| Growth protocol |
CD4+CD45RO+ cells were sorted from HC PBMC and JIA patient SFMC, activated with human T-activator CD3/CD28 dynabeads (1 cell: 3 beads) and cultured for 16h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAeasy kit (Qiagen).
Sample preparation was performed using TruSeq stranded total RNA with ribo-zero globin sample preparation kit (Illumina) and samples were sequenced 75bp single-end on Illumina NextSeq500 (Utrecht DNA sequencing facility).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sample demultiplexing and read quality assessment was performed using BaseSpace (Illumina) software.
Reads were mapped to the human reference genome (hg19) using TopHat v2.0.9 (tophat2 -p 8 --library-type fr-firststrand -G hg19.gtf).
Transcripts were assembled using CuffLinks v2.2.1 with the reference gene annotation (hg19) as a guide.
Transcriptomes were merged using Cuffmerge after which differential gene expression analysis was performed using Cuffdiff.
Reads were quartile normalized (--library-norm quartile) and reads mapping to rRNA or tRNA were masked from the quantification using the -M option. Similarly quartile normalized count and FPKM tables were generated using Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files containing quartile normalized FPKM values
|
| |
|
| Submission date |
Jul 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Janneke Peeters |
| E-mail(s) |
j.g.c.peeters-7@umcutrecht.nl
|
| Organization name |
UMC Utrecht
|
| Street address |
Heidelberglaan 100
|
| City |
Utrecht |
| ZIP/Postal code |
3584CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE71595 |
RNA-sequencing of cells derived from the site of inflammation of Juvenile Idiopathic Arthritis patients |
| GSE71597 |
Epigenetic profiling and RNA-sequencing of Juvenile Idiopathic Arthritits (JIA) patients |
|
| Relations |
| BioSample |
SAMN03946193 |
| SRA |
SRX1127388 |
