|
| Status |
Public on Jun 29, 2020 |
| Title |
S04: mRNA_Male_Neu_04 |
| Sample type |
SRA |
| |
|
| Source name |
neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
tissue: neutrophils
description for exp id: 180111_0112_s05
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood was collected in heparinized tubes after venipuncture. Neutrophils were isolated at room temperature by density gradient followed by lysis method. For RNA purification, neutrophils were centrifuged at 1600rpm for 5 minutes and resuspended in 750 μL TRI reagent (Sigma, cat. no. 93289). RNA was isolated using Zymo Research Direct-zol RNA Miniprep kit (Zymo Research, cat. no. R2050)
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina, cat. no. 20020594)
RNA seq data were generated on Illumina HiSeq 3000 instrument according to the manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Raw sequencing data were processed with bcl2fastq/2.17.1 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
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 13, 2020 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Mariana J. Kaplan |
| Organization name |
NIH/NIAMS
|
| Department |
Systemic Autoimmunity Branch
|
| Lab |
Lupus Clinical Trials Unit
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE145229 |
Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism (bulkRNA-seq) |
| GSE145231 |
Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism |
|
| Relations |
| BioSample |
SAMN14091544 |
| SRA |
SRX7716755 |
