|
| Status |
Public on Jun 12, 2015 |
| Title |
JB6 |
| Sample type |
SRA |
| |
|
| Source name |
Neutrophil RNA from an adult
|
| Organism |
Homo sapiens |
| Characteristics |
age: adult
gender: male
cell type: Neutrophil
condition: healthy
|
| Treatment protocol |
Whole blood was drawn into 10 mL citrated Cell Preparation Tubes (Becton Dickinson, Franklin Lakes, NJ, USA). Cell separation procedures were started within one hour from the time the specimens were drawn. Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by subjecting the CPT tubes directly to density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis, and neutrophils were then immediately placed in TRIzol™ reagent (Invitrogen, Carlsbad, CA, USA) and stored at -80°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol™ reagent according to the manufacturer's directions. RNA was further purified using a RNeasy MiniElute cleanup kit including a DNase digest according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling : illumina RTA 1.18.64. FASTQ Generation : Casava 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1 with default paramters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Mar 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lisha Zhu |
| E-mail(s) |
lishazhu4508@gmail.com
|
| Organization name |
UT Health Science Center at Houston
|
| Street address |
7000 fannin st
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE66895 |
Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells [RNA-Seq] |
| GSE66898 |
Disease-Associated SNPs From non-Coding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells |
|
| Relations |
| BioSample |
SAMN03408092 |
| SRA |
SRX956540 |
