|
| Status |
Public on Aug 03, 2022 |
| Title |
SE+IFNy replicate 6 [RAW264.7] |
| Sample type |
SRA |
| |
|
| Source name |
RAW264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: RAW264.7
cell type: cell line, macrophage
treatment: 65-79*SE peptide and IFNy (5ng/ml)
treatment duration: 72 hours
|
| Treatment protocol |
RAW264.7 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 |
RAW264.7 cells grown in DMEM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Trizol and the Direct-ZolTM RNA miniprep from Zymo research. 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 HLA23
|
| Data processing |
Raw counts were attained using featureCounts from the Rsubread1.5.0p3 package.
Gencode-M12 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: Gencode-M12 (GRCm38.p5)
Supplementary_files_format_and_content: deSeq2_counts RAW264.7 cells_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 |
GPL17021 |
| Series (2) |
| GSE173875 |
The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope [RAW264.7] |
| GSE173877 |
The lupus susceptibility allele DRB1*03:01 encodes a disease driving epitope |
|
| Relations |
| BioSample |
SAMN19013983 |
| SRA |
SRX10775290 |
