|
| Status |
Public on Aug 03, 2022 |
| Title |
SE replicate 2 [THP-1] |
| Sample type |
SRA |
| |
|
| Source name |
THP-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
cell type: cell line, macrophage
treatment: 65-79*SE (100 μg/ml)
treatment duration: 72 hours
|
| Treatment protocol |
Differentiated THP-1 cells were treated with or without IFNγ (5 ng/ml) in the presence or absence of 15-mer peptides 65-79*0301 (LE), 65-79*0401 (SE) or 65-79*0402 (PE) (100 μg/ml) for 72 hrs. Medium was refreshed once at 48 hrs.
|
| Growth protocol |
THP-1 cells were grown with PMA (85 nM) for 3 days followed by 5 additional days without PMA prior to the experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with RNeasy mini kit from Qiagen. Genomic DNA was removed using the Turbo DNA-Free kit from Ambion. 200 ng total RNA was used to generate libraries with the Illumina TruSeq RNA Sample Prep Kit.
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 |
| |
|
| Description |
Labeled W
|
| Data processing |
Raw counts were attained using featureCounts from the Rsubread-1.6.1 package.
Gencode28-hg38 gene annotations using only uniquely aligned reads.
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05.
Genome_build: Gencode28-hg38
Supplementary_files_format_and_content: deSeq2_counts THP-1_IFNy LE_SE_PE.txt
|
| |
|
| Submission date |
May 04, 2021 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Joseph Holoshitz |
| E-mail(s) |
jholo@med.umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine - Rheumatology
|
| Street address |
1150 W Medical Center Dr
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE173876 |
The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [THP-1] |
| GSE173877 |
The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope |
|
| Relations |
| BioSample |
SAMN19013673 |
| SRA |
SRX10775160 |
