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| Status |
Public on Jun 18, 2016 |
| Title |
JIA patient 2_active_disease |
| Sample type |
SRA |
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| Source name |
CD4+ T cell
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| Organism |
Homo sapiens |
| Characteristics |
disease stage: JIA patient with active, untreated disease
tissue: blood
cell type: CD4+ T cell
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol™ reagent according to manufacturer's directions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific, Wilmington, DE) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc., Palo Alto, CA)
Samples libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit according to the manufacture's recommended protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
JIA patient with active, untreated disease
CD4TCell_ADT_2
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| Data processing |
Sequences were excluded for adapter contamination and low quality bases
Sequences were aligned to hg19 human reference genome using Tophat version 2.0.13
Gene expression abundance was calculated by HTSeq count version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample
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| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
JAMES JARVIS |
| Organization name |
UNIVERSITY AT BUFFALO
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| Department |
PEDIATRIC
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| Lab |
JAMES JARVIS
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| Street address |
875 ELLICOTT STREET 8026
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| City |
BUFFALO |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE83415 |
CD4+ T Cells Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis (JIA) |
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| Relations |
| BioSample |
SAMN05254951 |
| SRA |
SRX1848803 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2202554_JB115_htseq.count.txt.gz |
231.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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