|
| Status |
Public on May 09, 2018 |
| Title |
mRNA_lupus_LH__TBR_4 |
| Sample type |
SRA |
| |
|
| Source name |
Human whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
diagnosis: Lupus
vascular phenotype: High TBR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood was collected by venipuncture in PAXgene Blood RNA Tubes (BD Diagnostics) and stored at -80C. RNA was isolated using Paxgene Blood RNA Kit (Qiagen, Inc.)
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina). RNA seq data were generated on Illumina HiSeq 2500 or 3000 instruments according to the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
exp ID: 161220_0011_s09
sample name: S09
|
| Data processing |
alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
RPKM calculation: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: hg19
Supplementary_files_format_and_content: excel for a RPKM file
|
| |
|
| Submission date |
Feb 15, 2018 |
| Last update date |
May 09, 2018 |
| Contact name |
Hong-wei Sun |
| Organization name |
NIAMS
|
| Department |
Office of Science & Technology
|
| Lab |
Biodata Mining & Discovery Section
|
| Street address |
9000 Rockville Pile
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE110685 |
Low density granulocytes and their gene signature associate with vascular inflammation and coronary atheroclerosis in systemic lupus erythematosus patients |
|
| Relations |
| BioSample |
SAMN08546675 |
| SRA |
SRX3703089 |
