|
| Status |
Public on Oct 23, 2018 |
| Title |
mRNA_HC_NDN_1 |
| Sample type |
SRA |
| |
|
| Source name |
Human neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neutrophils
healthy control or papa: Control
sample id: S01
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Normal density neutrophils were isolated by dextran sedimentation from control and PAPA patients. LDGs were isolated by negative selection from the PBMC fraction. Cells were resuspended in TriPure and RNA was isolated using the Zymo RNA Miniprep Kit.
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina)
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 |
| |
|
| Description |
171213_0108_s02
|
| Data processing |
Raw sequencing data were processed with bcl2fastq 1.8.4 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 |
Jul 16, 2018 |
| Last update date |
Oct 23, 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) |
| GSE117168 |
Dysregulated neutrophil responses and neutrophil extracellular trap formation and degradation in PAPA syndrome |
|
| Relations |
| BioSample |
SAMN09665979 |
| SRA |
SRX4394771 |
