|
| Status |
Public on Nov 01, 2022 |
| Title |
Transcriptional profiling of peripheral neutrophils from BD patinet 5 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood
cell line: peripheral neutrophil
cell type: /
genotype: /
treatment: BD
batch: 5
age: 35
Sex: male
oral ulcer: Yes
genital ulcer: No
gastrointestinal involvement: No
erythema nodule: Yes
ocular involvement: No
vascular involvement: Yes
cns involvement: No
arthritis: No
|
| Treatment protocol |
Peripheral neutrophils were isolated from blood by density gradient centrifugation and then resuspended in PBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BD patients
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: count_matrix.csv concludes combined csv file of matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: sample_info.csv concludes sample information
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Wenjie Zheng |
| E-mail(s) |
wenjzheng@gmail.com
|
| Organization name |
Peking Union Medical College Hospital
|
| Street address |
No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE205867 |
transcriptional profiling of neutrophils in Behcet's Disease (BD). |
|
| Relations |
| BioSample |
SAMN28968089 |
| SRA |
SRX15671946 |
