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Sample GSM1841081 Query DataSets for GSM1841081
Status Public on Sep 15, 2015
Title JIA_C_plus
Sample type SRA
 
Source name Synovial Fluid
Organism Homo sapiens
Characteristics diagnosis: JIA patient
tissue: Synovial Fluid
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 SAMN03946202
SRA SRX1127397

Supplementary file Size Download File type/resource
GSM1841081_JIA_C_plus_FPKMquartile.txt.gz 510.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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